[gmx-users] Assigning OPLS-AA atom types to new ligands

David spoel at xray.bmc.uu.se
Fri Apr 1 19:40:54 CEST 2005

On Fri, 2005-04-01 at 18:35 +0200, Shang-Te Danny Hsu wrote:
> It is a general question of the use of OPLS-AA force field.
> I would like to assign OPLS-AA atom types, which are a few hundreds, to 
> atoms in residues that are not defined in the GROMACS library. Unlike 
> GROMOS, which has only 45 atom types, it is not trivial to me as to how 
> one can decide which atom type is to be assigned to a certain chemical 
> group, although each atom type has a simple description.
> For instance, how can I create a GROMACS topology file of a 
> N-acetyl-glucoseamine (GlcNAc) with OPLS-AA atom types?
> I failed to find a manual for OPLS-AA describing a general procedure of 
> such assigning process. Can someone explain or direct me to resolve this 
> problem?
Check the file ffoplsaa.atp, which will give you suggestions for atom
types in similar groups. The OPLS papers have quite clear instructions
on how to compute charges using ab initio methods.
> Thanks, Danny
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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