Re: Protein-ligand simulation

From: James Starlight (
Date: Fri Jun 28 2013 - 04:21:45 CDT

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
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

#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


This is parameters from the PSFgen

package require psfgen
topology top_all36_prot.rtf
topology top_all36_na.rtf

and that is from the conf file

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


2013/6/28 Irene Newhouse <>

> 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:
> To:;
> 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 <>
> 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 <>
> 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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