Re: Subject: Re:Re: New partial charges after patching

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Jun 19 2014 - 10:11:28 CDT

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
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> 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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