[gmx-users] intermolecular distance restrains
nahren manuel
meetnahren at yahoo.com
Fri Sep 3 11:35:46 CEST 2010
Dear Gromacs Users,
Justin, I took your advice and using 4.5.1.
I have attached the PDB file for your consideration.
http://www.4shared.com/file/RwF_wuja/chainABCRST.html
Command : newpdb2gmx -f chainABCRST.pdb -p dimertop.top -o dimerpdb.pdb -chainsep interactive -ignh
8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta (forcefield selected)
6: None (water model)
Reading chainABCRST.pdb...
Read 6636 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with
chain starting with residue LYS284 (chain id 'B', atom 1445 N)? [n/y]
y
Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with
chain starting with residue LYS567 (chain id 'C', atom 2889 N)? [n/y]
y
Merge chain ending with residue LEU710
(chain id 'C', atom 4332 OXT) with
chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y]
n
Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with
chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y]
y
Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with
chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y]
y
Program newpdb2gmx, VERSION 4.5.1
Source code file: pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms
while sorting atoms.
*********
But this selection works (for the same above command, 1 )
Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with
chain starting with residue LYS284 (chain id 'B', atom 1445 N)? [n/y]
y
Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with
chain starting with residue
LYS567 (chain id 'C', atom 2889 N)? [n/y]
n
Merge chain ending with residue LEU710 (chain id 'C', atom 4332 OXT) with
chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y]
y
Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with
chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y]
n
Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with
chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y]
y
*************************
After ABC , I include a 'TER', then start chain RST, and make 'chainsep ter'
2. newpdb2gmx -f chainABCRSTter.pdb -p dimertop.top -o dimerpdb.pdb -chainsep ter -ignh
Program newpdb2gmx, VERSION 4.5.1
Source code file: pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms
while sorting atoms.
The
residue are not in sequential Order , but i dont think that is the problem here.
Thank you.
Best,
nahren
--- On Fri, 9/3/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] intermolecular distance restrains
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Date: Friday, September 3, 2010, 3:18 AM
nahren manuel wrote:
>
> Dear Gromacs Users,
>
> The problem actually is mine is a hexamer, ARBSCT (chains). I want RST to be merged into a single molecular topology. I am either able to merge RS or ST or RT but not the trimer as such.
>
How is the .pdb set up? Does it have both chain ID's and TER delimiters? What was your pdb2gmx command line?
-Justin
> I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx.
>
> Best,
> nahren
>
> --- On *Thu, 9/2/10, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] intermolecular distance restrains
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Thursday, September 2, 2010, 8:09 PM
>
>
>
> nahren manuel wrote:
> > Dear Gromacs Users,
> >
> > I am presently using gromacs4.5 beta(since I want implicit
> solvent). I
>
> No need to use a beta version, the official 4.5 has been released.
>
> > wish to apply intermolecular distance restraints.
> > To my surprise there is no merge option in pdb2gmx (although
> pdb2gnx -h, says it has). So is there a new alternative to create
> intermolecular distance restrains.
> >
>
> Use pdb2gmx -chainsep.
>
> -Justin
>
> > Best,
> > nahren
> >
> >
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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