[gmx-users] Re: gmx-users digest, Vol 1 #609 - 8 msgs

Chris O'Brien obrien at CLEMSON.EDU
Mon Apr 7 14:15:01 CEST 2003

>Message: 5
>Date: Fri, 07 Feb 2003 17:07:05 +0100
>From: Anton Feenstra <feenstra at chem.vu.nl>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Multiple dihedral types in .rtp file
>Reply-To: gmx-users at gromacs.org
>Chris O'Brien wrote:
> > Hello all,
> >
> > I am trying to model a polymer using GROMACS.  Because it uses a
> > non-standard residue, I am adding one (actually 5) to the ffgmx.rtp
> > file.  I would like to use both a Ryckaert-Bellemans and a periodic
> > function to best describe the dihedral rotation barriers.  What format
> > do I need to use to get this to work?  Can I just use two [ bondedtypes
> > ] lines at the beginning of the file that will only differ in the
> > dihedrals column?  Can I define bondedtypes specifically for each
> > residue?  However it is done, I want to make sure it won't interfere
> > with the built-in residues in the file because others will be using
> > GROMACS here as well.
>You can include explicit parameters directly in the .rtp file, which will
>only affect those residues. Using bondedtypes directives (in the ffgmxbon.itp
>file), you cannot define two functions on the same set of atoms. In stead
>of really explicit parameters in the .rtp, you can also use the method that
>is used in the Gromos forcefield (ffG43*), where in the ff*bon.itp a
>#define is used to attach parameters to a label, and this label is inserted
>in the .rtp file. This way, you will keep the separation between topology
>info (rtp) and parameters (ff*bon.itp).

Thank you for your help.  After some reading and trial-and-error work in 
gromacs, I have a series of related questions for the group on how exactly 
to implement the combined R-B and periodic functions and get them to work.

(1) I've seen it mentioned by this group that there is a glitch in pdb2gmx 
that causes it to overwrite multiple dihedrals defined in an rtp 
file.  Looking through the revision history, I didn't see that this had 
been addressed yet.  I'm running 3.1.3 and only a single periodic dihedral 
appears in my .top file when I use pdb2gmx.  Has it been changed in a newer 
version?  If not, is there any estimate for when it will be 
completed?  This glitch makes it difficult for me to sort out what I need 
to change to make gromacs work for me.  (I get a lot of "Can't perturb 
multiplicity" errors.)

(2) I am altering ffgmx.rtp.  Because this file wants type 1 (periodic) 
dihedrals, I am defining my periodic dihedrals there, and trying to use the 
#define statement to add the R-B dihedral definition.  In ffgmxbon.itp, I 
have added the line

#define RBDIH1 1.175 -10.32 7.56 23.79 -0.56 -11.07

and use this label (RBDIH1) in ffgmx.rtp.  (Unsurprisingly, maybe) pdb2gmx 
interprets this as 2 periodic dihedrals.  Since I can't change the [ 
bondedtypes ] function specifications, how do I make pdb2gmx know that I 
want a R-B dihedral?  Ideally, I would like to be set up so that I don't 
have to make any explicit changes to the resulting .top file after running 
pdb2gmx.  Basically, I'm not sure that I am using the #define statement 
correctly because I can't find any directions on its use, just a few simple 

(3) I think this problem will clear itself up by trial if (1) is addressed, 
but in terms of circumventing the "B topology" used in FEP, I simply need 
to supply duplicate definitions for all of the dihedrals defined in 
ffgmx.rtp so that the A and B topologies have the same multiplicity, right?

Thank you,
Chris O'Brien

Department of Chemical Engineering
Clemson University
Clemson, SC  29634-0909

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