[gmx-users] Re: converting pdb to gmx successfully
leafyoung81-group at yahoo.com
Wed Feb 8 07:30:53 CET 2006
Don't just be satisfied with smooth running of pdb2gmx. For NA simulation,
(6) in the "Important notes on using the AMBER ports" on ffamber's web page
shall also be taken care.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of David Mobley
Sent: Wednesday, February 08, 2006 8:33 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: converting pdb to gmx successfully
Amber FF is maintained by the Pande group so you could ask them. But
it hasn't been out particularly long, so I wouldn't be too terribly
surprised if no one has made these yet.
On 2/7/06, David Mathog <mathog at caltech.edu> wrote:
> Well I'm getting closer to "automatic" pdb->gmx but it's still
> more of a slog than it should be.
> 1. Run raw.pdb file through "reduce -BUILD" -> input.pdb
> (This puts on all required protons except, alas, for the ones
> at the N termini).
> 2. Run raw.pdb through "whatif". Copy the 3 lines for the 3 N
> terminal hydrogens into the first Amino acid residue (per chain)
> in input.pdb.
> 3. Use modified Amber ff (O -> O2 for all THY residues) and add
> that to the first position in FF.dat.
> 4. Run pdb2gmx (my own patched up version that automagically
> changes residue and atom names for Amber, to be posted for your
> use soon).
> The pdb2gmx runs successfully. The amount of manual cut and pasting
> has been reduced from a ton to just three lines.
> Unfortunately pdb2gmx won't by itself put on all the hydrogens
> Amber wants so specifying -ignh or feeding in raw.pdb directly doesn't
> The carboxyl end is wrong of course, since even if there's an OXT
> in the PDB file nothing useful shows up in the output gro file. In
> most cases it shouldn't matter much.
> The nucleic acid 5' end must be a OH, since the 5' models in the Amber
> ff set are all like that.
> The ASP/ASPH/GLU/GLUH interactive stuff works and properly ends up
> as the Amber ASP/ASH/GLU/GLH.
> Ideally it would be nice if pdb2gmx could generate the N and C termini
> all by itself. It looks like "all" that's needed for that are -n.tdb
> and -c.tdb files. However I don't know yet how to write those. Does
> anybody have these already for the Amber FF files?
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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