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

Anton Feenstra feenstra at chem.vu.nl
Thu Apr 10 09:00:05 CEST 2003

Chris O'Brien wrote:
> 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 examples.

It's from the cpp pre-processor. 'man cpp' will give you some info on
most systems. Basically, the syntax of your example is correct.
Any line in the form of

#define LABEL any amount of text on a single line

will cause 'LABEL' in all subsequent text to be replaced
by 'any amount of text on a single line'.

As for the 'bondedtypes' question, do you need all the other building
blocks at the same time in pdb2gmx as those for your polymer? Even
if you would have the polymer together with a protein in your system,
you could make separate .top files with separate runs of pdb2gmx,
change them into .itp files, and combine all in a single .top file
with appropriate #include's and entries in the [ system ] section.

That way, you can have your own 'ffpolymer*.*' files, which you use
with pdb2gmx to generate your polymer topology, with whatever
[ bondedtypes ] you like.
This will fail, of course, if your polymer connects covalently to
a protein, or to some residues. E.g. for glycosilation of a protein,
this would not help.

> (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?

Sounds about right.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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