Ok, thanks François,
Stephane
________________________________________
De : FyD [fyd.q4md-forcefieldtools.org]
Date d'envoi : jeudi 23 mai 2013 12:49
À : AMBER Mailing List
Objet : Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ?
Hi Stephane,
> It is possible to generate a mol2, if I have only a PDB of my
> molecule and a file generated by the RESP program. If yes, how ?
For a whole molecule this is quite simple:
You remove the set of charge values from the mol2 file generated by
R.E.D., and replace it by the corresponding set of values taken from
the RESP output (be sure that the atom order is the same in the mol2
and RESP output files); this is straightforward by using the "Block
selection" mode in the kate or geany text editor...
For a molecular fragment just select the 'right' block of atoms from
the RESP output.
Another approach would be to modify the source code of R.E.D. III.x
(i.e. add the required keywords for MEP computation for the RESP-A1
charge model) and simply re-run R.E.D. either in its mode 2 or in
Re_fit mode...
regards, Francois
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Received on Thu May 23 2013 - 04:00:03 PDT
