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
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