From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Jul 11 2014 - 12:19:21 CDT
Any news on this? I can have a look at your patch if you post it.
On 06/19/2014 11:11 AM, Kenno Vanommeslaeghe wrote:
> The sum of the combined entity should be integer (0) no matter what. In
> the specific case of the CHARMM amide bond, even the separate residues
> still have an integer (0) charge. If these conditions are not satisfied,
> then you did something wrong.
> On 06/19/2014 04:21 AM, Sadegh Faramarzi Ganjabad wrote:
>> Hi Kenno
>>
>> Thanks again for considering my case. I know I have to assign amide
>> charges to those atoms, but my question is that; before patch, each of two
>> residues had integer total charges (-1 and +1). If I assign amide partial
>> charges to connected atoms, the sum of atomic charges of those two
>> residues won't be integer anymore. Isn't that in issue?
>>
>> Regards
>> Sadegh
>>
>>
>> On Tue, Jun 17, 2014 at 11:46 AM, namd-l digest
>> <owner-namd-l-digest_at_ks.uiuc.edu <mailto:owner-namd-l-digest_at_ks.uiuc.edu>>
>> wrote:
>>
>>
>> namd-l digest Tuesday, June 17 2014 Volume 01 : Number
>> 1409
>>
>>
>>
>> In this issue:
>>
>> Re: namd-l: New partial charges after patching
>> Re: AW: AW: namd-l: How to refer to side-chain via tcl-force
>> scripting?
>> namd-l: alchemical free energy simulations with parmtop
>> namd-l: Reg : MD simulation with DMSO instead of water
>> Re: namd-l: Reg : MD simulation with DMSO instead of water
>> namd-l: Merging the two files......
>> Re: namd-l: Merging the two files......
>>
>> ----------------------------------------------------------------------
>>
>> Date: Mon, 16 Jun 2014 11:23:02 -0400
>> From: Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu
>> <mailto:kvanomme_at_rx.umaryland.edu>>
>> Subject: Re: namd-l: New partial charges after patching
>>
>> The answer to that question has not changed since last time you
>> asked it.
>>
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2591.html
>>
>> The recommendation is still to use standard CHARMM amide atom types and
>> charges. Among other places, the charges can be found in RESI NMA in
>> stream/toppar_all36_prot_model.str . When removing a nonpolar
>> hydrogen to
>> free up a valence for the purpose of creating a bond to another
>> nonpolar
>> group, we sum the charge of the hydrogen into the parent atom, as
>> documented at many places. Be careful when doing that, because in many
>> instances, atom types change when removing hydrogens.
>>
>> On 06/14/2014 05:15 AM, Sadegh Faramarzi Ganjabad wrote:
>> > Hello
>> >
>> > I have connected side chain of ASP residue to side chain of LYS by
>> a patch
>> > to get a cyclic peptide; an oxygen atom of ASP side chain and two
>> hydrogen
>> > atom of LYS are deleted and the resulting patch is
>> >
>> > 1HB1 1HB2
>> > \ /
>> > --1CB
>> > \
>> > 1CG==OD1
>> > \
>> > 2NZ- 2HZ1
>> > |
>> > 2HE2 - 2CE- 2HE1
>> > |
>> >
>> > However, I'm wondering how should I assign atomic partial charges
>> to this
>> > part of molecule. ASP was negatively charged before patch to LYS
>> which was
>> > positively charged. Do you have any idea about how to update partial
>> > charges after patch?
>> >
>> > Thanks in advance
>> > Sadegh
>>
>> ------------------------------
>>
>> Date: Mon, 16 Jun 2014 09:20:46 -0700
>> From: zeynab mohamad hoseyni <zmhoseyni_at_yahoo.com
>> <mailto:zmhoseyni_at_yahoo.com>>
>> Subject: Re: AW: AW: namd-l: How to refer to side-chain via tcl-force
>> scripting?
>>
>> Hi Norman,
>>
>> In addition to the way to suggested here, which works very well,
>> the tcl force tutorial has provided another way
>> (Example 3: Forcing a Subset
>> of Atoms ,TclForcesB )B
>>
>> TclForces
>> TclForces
>> View on www.ks.uiuc.edu <http://www.ks.uiuc.edu>
>> Preview by Yahoo
>> through which you may introduce a target pdb, marking all
>> the side-chains you are interested in and then opening
>> the pdb, reading the
>> lines and extracting the atoms in each side-chains in order to refer
>> to them
>> in the next steps.
>> I was wondering which way is more efficient, specially in
>> the case that you need to apply force on the side-chains of all
>> residues
>> containing in theB protein (397 residues in my case)?
>>
>> I went through the way
>> you suggested here and it works very slowly. I'm looking for a way
>> toB improveB the efficiencyB
>> significantly and I wonder if you can guide me.
>> Thanks in advance,
>> Zeynab
>>
>> B
>>
>>
>> On Friday, June 13, 2014 9:26 AM, Norman Geist
>> <norman.geist_at_uni-greifswald.de
>> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
>>
>>
>>
>> You need to source the
>> prepare
>> script to VMD. Afterwards source the resulting conf file within TCL
>> forces and
>> work with the b sidechainsb array.
>> B
>> Norman Geist.
>> B
>> Von:zeynab mohamad
>> hoseyni [mailto:zmhoseyni_at_yahoo.com <mailto:zmhoseyni_at_yahoo.com>]
>> Gesendet: Freitag, 13. Juni 2014 10:21
>> An: Norman Geist
>> Cc: Namd Mailing List
>> Betreff: Re: AW: namd-l: How to refer
>> to side-chain via tcl-force
>> scripting?
>> B
>> Hi Norman,
>> Looks great! thanks! just
>> one more question: sourcing the tcl
>> through the tcl-force script
>> isB differentB from to write it down directly in the
>> tcl-force script? Because
>> when
>> I write it down directly IB receiveB the error from which
>> I defer that
>> the script can not realize theB commands
>> regarding the side chain..
>> B
>> All the
>> Best,
>> Zeynab
>> B
>> On Friday, June 13, 2014 8:56 AM,
>> Norman Geist
>> <norman.geist_at_uni-greifswald.de
>> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
>> B
>> Guess
>> no! A good way to do it, is
>> do write a TCL script for VMD to prepare some kind
>> of config file containing
>> the information you need and source this
>> configuration within your TCLForces
>> script. Like (expects to have a molecule
>> loaded already):
>> B
>> prepare.tcl:
>> B
>> puts b Input) Molid?b
>> gets stdin molid
>> puts b Input) Resids?b
>> gets stdin
>> resids
>> B
>> array unset
>> sidechains; #save restart
>> array set sidechains
>> {}
>> foreach resid $resids
>> {
>> B B B B B B B B B B B B B B B
>> set sel [atomselect
>> $molid b resid $resid and sidechainb ]
>> B B B B B B B B B B B B B B B
>> set
>> sidechains($resid) [$sel get index]
>> B B B B B B B B B B B B B B B
>> $sel delete
>> }
>> B
>> set fp [open
>> b prepared.conf.tclb w]
>> puts $fp [list array
>> set
>> sidechains [array get sidechains]]
>> close $fp
>> puts b Info) Done,
>> youb re are
>> now prepared!b
>> B
>> So within your
>> TclForces script:
>> B
>> source
>> prepared.conf.tcl
>> #loop over sidechains
>> foreach resid [array
>> names sidechains]
>> {
>> B B B B B B B B B B B B B B B
>> puts b Now doing something with sidechain of
>> resid $resid having this atoms:
>> $sidechains($resid)b
>> }
>> B
>> Norman Geist.
>> B
>> Von:owner-namd-l_at_ks.uiuc.edu <mailto:Von%3Aowner-namd-l_at_ks.uiuc.edu>
>> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>] Im
>> Auftrag von
>> zeynab mohamad hoseyni
>> Gesendet: Freitag, 13. Juni 2014 07:53
>> An:
>> namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
>> Betreff: namd-l: How to refer to side-chain via tcl-force
>> scripting?
>> B
>> Dear all,
>> B
>> I need to impose force
>> on the side-chain of some
>> residues, using tcl-force scripting. Do you know if
>> the tcl-force
>> interface
>> provides any command so that you can refer to side-chain of the
>> desired
>> residue?
>> B
>> Thanks in advance for
>> your help,
>> Zeynab
>> B
>> ________________________________
>>
>> Diese E-Mail ist frei von Viren und
>> Malware, denn der avast! Antivirus Schutz ist aktiv.
>> B
>> B
>> ________________________________
>>
>> Diese E-Mail ist frei von Viren und
>> Malware, denn der avast! Antivirus Schutz ist aktiv.
>>
>> ------------------------------
>>
>> Date: Tue, 17 Jun 2014 10:35:59 +0100
>> From: Hannes Loeffler <Hannes.Loeffler_at_stfc.ac.uk
>> <mailto:Hannes.Loeffler_at_stfc.ac.uk>>
>> Subject: namd-l: alchemical free energy simulations with parmtop
>>
>> Hi,
>>
>> I am just looking through a few tutorials on how to do alchemical
>> relative free energy calculations and see that they are all based on
>> the
>> PSF topology file format. I wonder if this is a requirement with namd
>> or a AMBER parmtop file could be used instead.
>>
>> From what I understand there could be problems with the force fields
>> terms in the parmtop because the way it works in namd is to create the
>> morph pair as a single residue (and describe vanishing/appearing atoms
>> in an associated PDB file). But is it possible with a parmtop provided
>> the parmtop is created/manipulated accordingly? I guess this all boils
>> down to how namd generates the force field terms internally for the two
>> mutated molecules/fragments.
>>
>> Many thanks,
>> Hannes.
>> - --
>> Scanned by iCritical.
>>
>> ------------------------------
>>
>> Date: Tue, 17 Jun 2014 16:34:58 +0530
>> From: Akshay Bhatnagar <akshaybhatnagar2790_at_gmail.com
>> <mailto:akshaybhatnagar2790_at_gmail.com>>
>> Subject: namd-l: Reg : MD simulation with DMSO instead of water
>>
>> Can anyone please tell how can i solvate an amino acid in DMSO
>> instead of
>> water. Like from where i can get the parameter, topology, pdb and psf
>> files
>> for DMSO?
>>
>> Thank you
>> With Regards
>> Akshay Bhatnagar
>> PhD Student
>> BITS Pilani Hyderabad Campus
>>
>> ------------------------------
>>
>> Date: Tue, 17 Jun 2014 13:12:55 +0200
>> From: Axel Kohlmeyer <akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>>
>> Subject: Re: namd-l: Reg : MD simulation with DMSO instead of water
>>
>> On Tue, Jun 17, 2014 at 1:04 PM, Akshay Bhatnagar
>> <akshaybhatnagar2790_at_gmail.com <mailto:akshaybhatnagar2790_at_gmail.com>>
>> wrote:
>> > Can anyone please tell how can i solvate an amino acid in DMSO
>> instead of
>> > water. Like from where i can get the parameter, topology, pdb and
>> psf files
>> > for DMSO?
>>
>> like with any other (custom) molecule: from the published literature
>> and with a text and/or molecule editor program
>>
>> furthermore, you will likely also need to reparameterize the amino
>> acid, since the typical parameters are tuned for a specific(!) water
>> model. if people already criticize the change of water potentials as
>> inconsistent, you can easily imagine what the attitude towards
>> changing to a completely different solvent is going to be.
>>
>> axel.
>>
>> >
>> > Thank you
>> > With Regards
>> > Akshay Bhatnagar
>> > PhD Student
>> > BITS Pilani Hyderabad Campus
>> >
>>
>>
>>
>> - --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
>> http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA,
>> USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>> ------------------------------
>>
>> Date: Tue, 17 Jun 2014 11:00:09 -0400 (EDT)
>> From: Gurpreet Kaur Dhindsa <el2275_at_wayne.edu
>> <mailto:el2275_at_wayne.edu>>
>> Subject: namd-l: Merging the two files......
>>
>> Dear all,
>> I am trying to merge two different files, one contains 92000 atoms and
>> the other one has
>> 40000 atoms. I am using these commands in VMD
>> ::TopoTools::mergemols [list 1 2]
>>
>> 1,2 are the number of my pdb files in VMD main window.
>> At the end, I have total of 130000 atoms. VMD gives me the correct
>> atom number till 99000
>> but after that it starts giving me some type of alphabets.
>>
>> ATOM B 99998 B H1 B TIP3W5762 B B -120.414 B 60.831 B -4.134 B 0.00 B
>> 0.00 B B B WT1 B H
>> ATOM B 99999 B H2 B TIP3W5762 B B -121.121 B 60.076 B -5.310 B 0.00 B
>> 0.00 B B B WT1 B H
>> ATOM B 186a0 B OH2 TIP3W5764 B B -116.219 B 60.562 -10.104 B 0.00 B
>> 0.00 B B B WT1 B O
>> ATOM B 186a1 B H1 B TIP3W5764 B B -116.062 B 60.855 -11.001 B 0.00 B
>> 0.00 B B B WT1 B H
>> ATOM B 186a2 B H2 B TIP3W5764 B B -115.555 B 61.039 B -9.593 B 0.00 B
>> 0.00 B B B WT1 B H
>> ATOM B 186a3 B OH2 TIP3W5765 B B -122.951 B 57.343 B 13.115 B 0.00 B
>> 0.00 B B B WT1 B O
>> ATOM B 186a4 B H1 B TIP3W5765 B B -122.161 B 57.022 B 13.633 B 0.00 B
>> 0.00 B B B WT1 B H
>>
>> Can someone try merging the files with that number of atoms? Please
>> give me your suggestions.
>>
>> Thanks,
>> Gurpreet Dhindsa.
>>
>> ------------------------------
>>
>> Date: Tue, 17 Jun 2014 11:44:36 -0400
>> From: Aron Broom <broomsday_at_gmail.com <mailto:broomsday_at_gmail.com>>
>> Subject: Re: namd-l: Merging the two files......
>>
>> and why do you say this is wrong, have you been unable to use it for
>> your
>> next steps?
>>
>> The PDB format was made with apparently very little (if any) thought
>> towards flexibility. As a result, it has a fixed number of columns for
>> each piece of information, rather than a special separating character.
>> Since 5 columns are given to the atom number you can't go past
>> 99999. So
>> the solution to this is to start using alphabetic characters. I think
>> you'll find that this works fine for your purposes, and only very old
>> programs might have a problem reading those in.
>>
>> Another problem with these fixed columns is that residue and atom
>> names can
>> only be so many characters, leading to very obfuscated names in many
>> cases,
>> and a lot of unintentional overlap when mixing forcefields.
>>
>>
>> On Tue, Jun 17, 2014 at 11:00 AM, Gurpreet Kaur Dhindsa
>> <el2275_at_wayne.edu <mailto:el2275_at_wayne.edu>>
>> wrote:
>>
>> > Dear all,
>> > I am trying to merge two different files, one contains 92000 atoms
>> and the
>> > other one has
>> > 40000 atoms. I am using these commands in VMD
>> > ::TopoTools::mergemols [list 1 2]
>> >
>> > 1,2 are the number of my pdb files in VMD main window.
>> > At the end, I have total of 130000 atoms. VMD gives me the
>> correct atom
>> > number till 99000
>> > but after that it starts giving me some type of alphabets.
>> >
>> > ATOM 99998 H1 TIP3W5762 -120.414 60.831 -4.134 0.00 0.00
>> > WT1 H
>> > ATOM 99999 H2 TIP3W5762 -121.121 60.076 -5.310 0.00 0.00
>> > WT1 H
>> > ATOM 186a0 OH2 TIP3W5764 -116.219 60.562 -10.104 0.00 0.00
>> > WT1 O
>> > ATOM 186a1 H1 TIP3W5764 -116.062 60.855 -11.001 0.00 0.00
>> > WT1 H
>> > ATOM 186a2 H2 TIP3W5764 -115.555 61.039 -9.593 0.00 0.00
>> > WT1 H
>> > ATOM 186a3 OH2 TIP3W5765 -122.951 57.343 13.115 0.00 0.00
>> > WT1 O
>> > ATOM 186a4 H1 TIP3W5765 -122.161 57.022 13.633 0.00 0.00
>> > WT1 H
>> >
>> > Can someone try merging the files with that number of atoms? Please
>> give
>> > me your suggestions.
>> >
>> > Thanks,
>> > Gurpreet Dhindsa.
>> >
>> >
>> >
>>
>>
>> - --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>> ------------------------------
>>
>> End of namd-l digest V1 #1409
>> *****************************
>>
>>
>
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