[gmx-users] gromacs charges
v.gogonea at csuohio.edu
Mon Sep 30 18:36:59 CEST 2002
If charges for all OPLS atom types are specified in ffoplsaanb.itp,
does the reading format for ffoplsaa.rtp require to specify the
charges in the topology of the molecule. I mean do I have still to fill
in the charges in the rtp file? I saw that in ffoplsaa.rtp the charges
for all amino acids are specified even they are given in ffoplsaanb.itp.
If I need to introduce a new OPLS atom type (e.g. sulfonium ion
[SR3]+), what code should I give to it? Codes run up to opls_965 in
On Friday, September 27, 2002, at 01:00 PM, Erik Lindahl wrote:
> quantix1 at gmx.de wrote:
>> Dear Gromacs-Users,
>> I am completely new to Gromacs. Let's say, I'm still thinking about
>> it. My first question is, how charges for non-standard amino acids or
>> molecules are usually derived for the force field in Gromacs. Is
>> there a
>> procedure which is considered to be standard and gives the most
>> consistent results (like the HF/6-31G -> RESP for AMBER) ?
>> This should be enough before the weekend. Thanks in advance,
> When it comes to building new molecules, nothing beats the Jorgense
> OPLS-AA/L forcefield (yes, it's available in Gromacs even if the
> webpages don't mention it). The nice thing about OPLS is that all
> are designed and parameterized as "building blocks", so you can attach
> new functional group to e.g. a protein, and you will only have to
> the charge of one or two atoms. Check the file share/top/ffoplsaa.atp
> for comments on all the different atom types.
> OPLS charges are derived with CHELPG, and for proteins all the backbone
> dihedrals have been parameterized not only to reproduce the position of
> the minima, but the actual form of the energy landscape.
> The AMBER forcefield is on our todo-list, but we've never felt really
> motivated since OPLS/AA is better in most cases.
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