From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jun 28 2013 - 17:43:24 CDT
In this case the problem is mixing force fields used for building the topology vs. running the simulation (Kenno was probably alluding to this by telling you to look at the atom types). HB in charmm22 became HB1 in charmm36. Again, I strongly advise working through tutorials, reading papers, etc. more carefully.
On Jun 28, 2013, at 4:12 PM, Kenno Vanommeslaeghe wrote:
> James,
>
> I think you're confused between atom *names* (the first column in the topology file) and atom *types* (the second column). In line with what JC said, I would recommend reading documentation and asking questions of senior people in your group (or your advisor) before resorting to the mailinglist.
>
> Cheers,
>
> Kenno.
>
> On 06/28/2013 03:55 PM, James Starlight wrote:
>> I noticed that HB atom (presented both in topology and in my pdb) present
>> in the LEU ILE THR and VAL
>>
>> I've already tried to make aliases
>>
>> pdbalias atom VAL HB1 HB
>> pdbalias atom ILE HB1 HB
>> pdbalias atom LEU HB1 HB
>> pdbalias atom THR HB1 HB
>>
>> but output pdb have still HB in that residues which are absent in the
>> parameter file.
>>
>> James
>>
>> 2013/6/28 Irene Newhouse <einew_at_hotmail.com <mailto:einew_at_hotmail.com>>
>>
>> Take a look at the protons called HB in your system. The type is in
>> one of the columns of your final pdf. Then take a look at the same
>> position in the topology file you're using & see what it's supposed to
>> be called. Alias it like HIS HSE. If that's not the problem, figure
>> out the H type in your parameter file which it most closely resembles,
>> & alias it to that, or take a look at different versions of the
>> parameter files & see if you can find it somewhere.
>>
>> Irene
>>
>> --------------------------------------------------------------------------
>> Date: Fri, 28 Jun 2013 13:21:45 +0400
>>
>> Subject: Re: namd-l: Protein-ligand simulation
>> From: jmsstarlight_at_gmail.com <mailto:jmsstarlight_at_gmail.com>
>> To: einew_at_hotmail.com <mailto:einew_at_hotmail.com>; namd-l_at_ks.uiuc.edu
>> <mailto:namd-l_at_ks.uiuc.edu>
>>
>>
>> Dear Irene,
>>
>>
>> thanks for suggestion.
>>
>> According to the PSFgen manual I've splited ligand and protein into
>> two separate pdb files.
>>
>> Than I've applied parametrization (using 27 params for protein and
>> nucleotide 36 params for cGMP-ligand).
>>
>> package require psfgen
>> resetpsf
>> topology top_crq_final.inp
>> topology top_all27_prot_lipid.inp
>> topology top_all36_na.rtf
>> pdbalias residue HIS HSE
>> segment A {
>> pdb input.pdb
>> first NTER
>> last CTER
>> }
>> coordpdb input.pdb A
>>
>> guesscoord
>> #patch NTER A:1
>> #patch CTER A:424
>>
>> segment B {
>> pdb ligand.pdb
>> first NONE
>> last NONE
>> }
>>
>> coordpdb ligand.pdb B
>>
>>
>> patch CY35 B:1 B:1
>> regenerate angles dihedrals
>>
>> writepsf start.psf
>> writepdb start.pdb
>>
>> Than I solvated my system and made minimization without any warnings.
>> Does this complex preparation correct ?
>>
>>
>> 2) I've forced with the parametrisatrion of the same complex using
>> Charm 36 protein's params. I have no any problems with the psfgen but
>> during loading my complex in NAMD for energy minimisation I've obtained
>>
>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB
>>
>> This is parameters from the PSFgen
>>
>> package require psfgen
>> resetpsf
>> topology top_all36_prot.rtf
>> topology top_all36_na.rtf
>>
>> and that is from the conf file
>>
>> #forcefield
>> paratypecharmm on
>> parameters par_all36_prot.prm
>> parameters par_all36_na.prm
>>
>>
>> Should I rename each HB atom in my input files or is the any other
>> suggestions?
>>
>> James
>>
>> 2013/6/28 Irene Newhouse <einew_at_hotmail.com <mailto:einew_at_hotmail.com>>
>>
>> You don't start the psfgen process with a solvated, ionized
>> structure for NAMD. You start with a pdb file that has no H
>> atoms. In your case, it contains the protein/ligand complex. Now
>> edit that pdb file into 2 pieces, one for the protein & one for
>> the ligand. You then write a psfgen script along the lines
>> described to you earlier in this thread. You do the psf
>> procedure for BOTH units AT THE SAME TIME. Your output will be a
>> new pdb file with H and containing both the protein & ligand, and
>> its associated psf file. There is no way to merge 2 separate psf
>> files. After you run psfgen, you solvate & ionize your structures
>> with VMD. You MUST read in BOTH the pdb & the psf files that you
>> generated with psfgen into VMD for solvating & ionizing. When you
>> are finished, you have a new set of pdb & psf files which are the
>> ones you use for NAMD. You do NOT incorporate them into the namd
>> conf file. You write their names into the NAMD conf file. The conf
>> file must also contain the name of the parameter file - if you
>> have an independent set of ligand parameters, there is no way I
>> know of to use 2 separate files. You'll have to edit the ligand
>> parameters into the NAMD parameter file you intend to use for the
>> protein. You will have to transfer 4 files to the computer on
>> which you intend to run NAMD from the computer you used to prepare
>> your system: the NAMD conf file, the final pdb file, the final psf
>> file & the parameter file.
>>
>> Hope this helps.
>> Irene Newhouse
>>
>> --------------------------------------------------------------------------
>> Date: Fri, 28 Jun 2013 08:35:21 +0400
>> Subject: Re: namd-l: Protein-ligand simulation
>> From: jmsstarlight_at_gmail.com <mailto:jmsstarlight_at_gmail.com>
>> To: gumbart_at_ks.uiuc.edu <mailto:gumbart_at_ks.uiuc.edu>;
>> namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
>>
>>
>> I still be thankful to everyone who can provide me with the NAMD
>> tutorial for the protein-ligand simulation and subsequent analysis
>> ( In particular I'm interesting in the dynamics of the Hbonds
>> between protein and ligand during simulation RUN).
>>
>>
>> James
>>
>> 2013/6/28 JC Gumbart <gumbart_at_ks.uiuc.edu
>> <mailto:gumbart_at_ks.uiuc.edu>>
>>
>> You're asking many questions that may be best answered by
>> reading through the various tutorials, user guides, previous
>> posts on the mailing lists, and literature as well as some
>> trial and error. Then if something still is unclear, you
>> should come back here and ask, explaining what you tried and
>> what didn't work. I don't mean to discourage you by any
>> means, but rather ENCOURAGE you to avail yourself of the
>> numerous resources into which a great deal of time was already
>> devoted. Personally, I feel like this will be more useful in
>> the long run.
>>
>> I sincerely hope I don't send you running back to gromacs! I
>> understand a new program can be daunting (ever try to run
>> charmm for the first time? ;) But the tutorials are immensely
>> helpful, I assure you.
>>
>>
>> On Jun 27, 2013, at 2:18 PM, James Starlight wrote:
>>
>> Kenno,
>>
>> thanks again for suggestion.
>>
>> By the way could someone tell me how ligand topology (psf
>> file) should be included in the namd's conf file ? For
>> example I have system consited of solvated protein with
>> ions (for that system I have psf file).
>> Than I've done parametrization for my ligand (obtaining
>> pdb as well as psf files ). Assuming that my ligand is in
>> the correct pose regarding protein I can merge both pdb
>> files. But how I should merge both psf files ( or should
>> I include both of them in the conf file separately ? )
>>
>> Thanks for help,
>>
>> James
>>
>> 2013/6/27 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu
>> <mailto:kvanomme_at_rx.umaryland.edu>>
>>
>> On 06/27/2013 01:16 AM, James Starlight wrote:
>>
>> psfgen) total of 34 atoms
>> psfgen) total of 37 bonds
>> psfgen) total of 66 angles
>> psfgen) total of 99 dihedrals
>> psfgen) total of 3 impropers
>> psfgen) total of 0 cross-terms
>>
>>
>> Those are the correct sums as also seen in CHARMM.
>>
>>
>> Here you can see that dihedrals and angles for new
>> bond were also included
>> in the topology new bond between O3 and P looks
>> strange :)
>>
>>
>> Can you be a bit more specific? What looks strange
>> about this bond?
>>
>> Cheers,
>>
>> Kenno.
>>
>>
>>
>>
>>
>>
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