[gmx-users] intermolecular distance restrains
Justin A. Lemkul
jalemkul at vt.edu
Fri Sep 3 14:13:02 CEST 2010
I would suggest filing a bugzilla. It appears that the -chainsep option is not
as flexible as might be desired.
-Justin
nahren manuel wrote:
> 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
> </mc/compose?to=jalemkul at vt.edu>>/* wrote:
> >
> >
> > From: Justin A. Lemkul <jalemkul at vt.edu
> </mc/compose?to=jalemkul at vt.edu>>
> > Subject: Re: [gmx-users] intermolecular distance restrains
> > To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org </mc/compose?to=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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
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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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