AMBER Archive (2009)

Subject: [AMBER] Re: [Contact q4md] qurey reagarding RED Server

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Jun 13 2009 - 03:08:26 CDT

Dear Subarna Thakur,

> I want to use the RED server for charge calculation but I have a
> query. I am currently working in molecular dynamics of a protein
> with Fe4 S4 cluster. I have the pdb file of the Fe-S cluster.I want
> to know whether is it possible to calculate charges of Fe and S atom
> of the Fe-S cluster with R.E.D server.

Yes, indeed, you could try to use R.E.D. Server. However, two comments:

- The best bet might be to use R.E.D. Server in its "Mode 2";
i.e. see: http://q4md-forcefieldtools.org/REDS/popup/popmodes.php
This means you get the optimized geometry for your complex without
R.E.D. Server
& you load the corresponding QM output as input in R.E.D. server with
the P2N input file.
Moreover, here, you might consider a specific QM program for this
geometry optimization step.
See http://q4md-forcefieldtools.org/REDS/faq.php#12

- That being said, we are going to release a specific approach for
RESP charge derivation of metal complexes. However, this is not yet
available:
See: http://q4md-forcefieldtools.org/REDS/popup/news.php

regards, Francois

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber