[gmx-users] how to create tpr file from pdb created with Hyperhem for using with OPLS

[Mark Abraham]

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 
friend here.

> 2) Let's say I have top and gro created using PRODRG server and JML 

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 
is broken.

> 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/Steps_to_Perform_a_Simulation, 
http://wiki.gromacs.org/index.php/Parameterization, 
http://wiki.gromacs.org/index.php/Topology_File, and/or chapter 5 of the 
manual.

> 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?

Mark