Re: Protein-ligand simulation

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Jun 28 2013 - 16:12:50 CDT

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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