[gmx-users] gromos parameterisation in OPLS
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 16 17:59:34 CEST 2008
Changing the atomtypes will only work if you have explicit inclusion of
all hydrogens in your PRODRG-generated topology. Since the PRODRG
server outputs a GROMOS-based .itp file, this is unlikely unless your
molecule contains only polar or aromatic groups. If we're still talking
about CHAPS or cholesterol, this will not be the case. You will have
nonpolar groups that, within GROMOS, are atomtype CH1, CH2, etc., but
OPLS will not have these UA representations.
I'm not sure what you mean in the last sentence. Nothing in this
process will be automatically generated for you. You're building your
topology by hand. Inclusion of "ffoplsaa.itp" will tell grompp which
parameters (bonded and nonbonded) apply to your molecule. Calling
"ffoplsaa.itp" will not tell any Gromacs program to automatically detect
and generate bonds, dihedrals, etc.
The only way to have "automatic" generation of these parameters is to
build an .rtp entry for your molecule that contains all of this
information as well, and process your structure with pdb2gmx. This is
just as much work as building the topology yourself, I think.
ANINDITA GAYEN wrote:
> I came to know from the mailing list that if i only change the atomtype in the output itp file of PRODRG2 and put the charges as optimised by Gaussian; provided i include #include ffoplsaa.itp in the .top file of the new molecule and just keep the atom mumbers in [bonds], [pairs], [angles] and [dihedrals] as found in the the all atom pdb of PRODRG2, the resultant top file will be a top file in OPLS format. It was also stated there in the mailing list that for the atom numbers mentioned the opls staff will put the parameter values necccesary for the [bonds], [angles] etc.
> Is the approach right?
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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