From: Spitaleri Andrea (spitaleri.andrea_at_hsr.it)
Date: Fri Nov 08 2013 - 01:09:33 CST

Hi,
we recently published a protocol to use gromacs trajectory to calculate MM/PBSA. You may think to convert dcd to trr/xtc and try it.

let me know if you want it

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046902

hope it helps

and

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Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
Basilica San Raffaele, 3P 34R
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
www.biomolnmr.org
Tel: 0039-0226434348
Fax: 0039-0226434153
________________________________________
Da: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] per conto di Ramin Ekhteiari [ramin_ekh_at_yahoo.com]
Inviato: mercoledý 6 novembre 2013 9.56
A: vmd-l_at_ks.uiuc.edu; namd-l_at_ks.uiuc.edu
Oggetto: vmd-l: MM-PBSA calculation

Hi dears,

I did a MD simulation for my system by employing NAMD code and got dcd and other output files, but now I am trying to do a MM-PBSA calculation for this system, so can someone advise me on how to do these calculation via vmd?

Would be grateful for any advice.

Cheers,
Ramin