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.
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 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?
3) Moreover after creating top and gro using PRODRG server I chose to do
everything with gmx ff, 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) 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.
I'm using Gromacs3.3
Thank you in advance
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