[gmx-users] how to create tpr file from pdb created with Hyperhem for using with OPLS
Mark.Abraham at anu.edu.au
Tue Jan 15 23:47:14 CET 2008
Egidijus Kuprusevicius wrote:
> Dear Gromacs developers, I have some very simple questions on how to get
> the file (tpr) wich could be run on Gromacs (MD). With Hyperhem I have
> drawn the target molecule, I obtained ent file containing ATOM and
> CONNECT sections:
> 1) What should I change in this ent file to be able to run this file
> with pdb2gmx (by renaming to pdb) to obtain top and gro? I want to use
> OPLS ff.
If Hyperchem can't write a .pdb file natively, then complain at its
developers or pick a new molecule builder. Else google might be your
> 2) Let's say I have top and gro created using PRODRG server and JML
> using ffgmx. What I should change in my gro and top or itp (if I choose
> to create it) to be able to create tpr? I know expicitly all OPLS files
PRODRG server doesn't output an OPLS-compatible .top, so your strategy
> like itp (bn and nonbn), atp, rtp, n/c terminals (tdb), hdb. I know how
> to describe atoms types and bonds for my own molecule, but do not know
> how to describe dihedrals (proper and unproper)...it looks something
> like that - C +N O H impropers_O_C_X_Y ... what does it stand for and
> what are basic rules for constructing them?
I can't work out what you're trying to do here. Check out
http://wiki.gromacs.org/index.php/Topology_File, and/or chapter 5 of the
> 3) Moreover after creating top and gro using PRODRG server I chose to do
> everything with gmx ff,
Don't, it's deprecated. The PRODRG beta server might be better.
> but after creating box and solving this molecule
> in the water I couldn't get tpr file using grompp. I have got the error
> message that nr of atoms in top(=1500) doesn't match that one in
> gro(=0). I have tried to follow recomendations in a wiki errors section,
> but nothing helped me. So why some steps I was able to accompish (it
> indicates that my cpp on Unix can recognize EOL of Windows)
What is indicating to you that cpp is running correctly?
> and by
> runing grompp in order to get tpr I have got this message (I checked the
> nr in gro and top - both matched)? I have no more ideas what to do.
Checked what number?
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