[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.


> Hi,
> 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
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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