Re: Protein-ligand simulation

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Sat Jun 29 2013 - 00:02:32 CDT

1) I telling only about atom names.

2) I didnt mixed parameters sets from different charm sets.

The HB name is present in the top_all36_prot.rtf

E.g

RESI ILE 0.00
GROUP
ATOM N NH1 -0.47 ! | HG21 HG22
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | CG2--HG23
ATOM HA HB1 0.09 ! | /
GROUP ! HA-CA--CB-HB HD1
ATOM CB CT1 -0.09 ! | \ /
ATOM HB HA1 0.09 ! | CG1--CD--HD2
GROUP ! O=C / \ \
ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3
ATOM HG21 HA3 0.09
ATOM HG22 HA3 0.09
ATOM HG23 HA3 0.09
GROUP
ATOM CG1 CT2 -0.18
ATOM HG11 HA2 0.09
ATOM HG12 HA2 0.09
GROUP
ATOM CD CT3 -0.27
ATOM HD1 HA3 0.09
ATOM HD2 HA3 0.09
ATOM HD3 HA3 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG1 CB CG2 CB CD CG1
BOND N HN N CA C CA C +N
BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21
BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N

3) Please show me correct syntax for PSFGEN to make aliases for HB and HB1
( I want to consider all HB as the HB1 in the final pdb and topology)

James

2013/6/29 Irene Newhouse <einew_at_hotmail.com>

> Do a grep for the string HB in your parameter file & see if you find any.
> If not, that's your problem.
> Irene
>
> ------------------------------
> Date: Fri, 28 Jun 2013 23:55:55 +0400
>
> Subject: Re: namd-l: Protein-ligand simulation
> From: jmsstarlight_at_gmail.com
> To: namd-l_at_ks.uiuc.edu
>
>
> 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>
>
> 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
> To: einew_at_hotmail.com; 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>
>
> 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
> To: gumbart_at_ks.uiuc.edu; 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>
>
> 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>
>
> 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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