Egidijus Kuprusevicius wrote:
Thanks Mark,
but your first answer didn't help me at all. I want to create pdb
manually which will work with gromacs pdb2gmx comand in order to get gro
and top using OPLS, and seeking for some clues. It doesn't matter if it
is Hyperchem or JME or MOL, I need a proper pdb which will be
understandable to Gromacs.
We being asked about converting .ent formats :-) I think I suggested as
good a strategy as any. About a minute's googling reveals that Hyperchem
can write a .pdb format.
I know that PRODGR is not compatible with OPLS, that's why I am
asking how to change gro and top to enable them to be compatible with OPLS
That's a better question. Atom names and residue names need to be
consistent with what is in the force field files. There are standard
names for these, and if your PDB-generator uses them then you can feed
them to pdb2gmx, choose oplsaa and probably do OK. PRODRG is useless
here. If you need non-standard residues, then see the GROMACS wiki page
on Parameterization.
The same story and with beta files (with ff43a1.itp)
I'm trying to run MD using OPLS with my own molecule solved in the
water, for that I was trying to create mymolecule.itp database file, and
in order to do so I need to know how to describe correctly dihedrals (in
OPLS standart)
Chapter 5 in the manual describes the format, chapter 4 describes the
functions the format defines.
'what indicates?' it's just simple logic if I use edited on Windows
files to produce new gro and updated top files on Unix, that indicates to
me that cpp have no errors in reading these files (may be I am wrong,
because I do not know how these files are processed during each of these
precesses - like genbox and editconf, probably it's different from
grompp?).
When replying to someone, please quote their words so that people know
what you're talking about. I partly remember, because I wrote them, but
hardly anybody else will.
number of molecules of whater in top x3+1(my molecule)xn(number of
atoms in that molec.)=total nr of atoms in gro file. (it would be in gro
let's say 1500 atoms, and in top let's say DGR=1 and SOL=490).
I know exist some short instructions how to do so, but I couldn't find
them in the manual.
P.S.these links provided are pointing to the empty sites.
I can't remember what you're talking about here.
Mark
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