[gmx-users] Questions about opls-aa force field for gromacs
spoel at xray.bmc.uu.se
Tue Feb 22 06:59:24 CET 2005
On Tue, 2005-02-22 at 12:42 +0800, zjim wrote:
> Dear all
> I am a gromacs user and i was trying to add some parameters for sugar
> to the opls-aa force field parameters which you provided on the
> gromacs web site. the parameters added are mainly base on two papers
> as follow:
> J Comput Chem 18:1955-1970 1997
> J Comput Chem 23:1416-1429 2002
> which i did was reasonable?
If these are compatible with OPLS and in particular with the recommended
TIP4P water model then the answer is yes.
> another question is how to edit the glucose monomer "residue topology"
> in the .rpt file. It is not a problem for editing the whole glucose
> topology, yet for the glucose monomer is a part of glucose molecule
> and is jointed between the preceding and next monomers.I don't know
> how to describe the joint atom as well as the angle and torsion
> involved it. i examined the animo acid monomers "residue topology" for
> they also joint one by one. i found the "-C" and "+N" may be taken as
> joint atom. Does that suit for glucose monomer "residue topology" also
> and how to do it?
Check the ffgmx and/or ffG43* rtp files and chapter 5 of the manual.
> please give me some advice, thank you very much!
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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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