Re: [AMBER] MMPBSA.py on single snapshot

From: Kasam, Vinod <vkasam.coh.org>
Date: Wed, 19 Sep 2012 15:25:13 -0700

Thank you Jason, it worked fine.

Vinod
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Wednesday, September 19, 2012 2:20 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py on single snapshot

On Wed, Sep 19, 2012 at 4:44 PM, Kasam, Vinod <vkasam.coh.org> wrote:

> Dear Amber users,
>
> I was able to use MMPBSA.py on a trajectory obtained from MD simulation,
> However, can some body tell me how to run MMPBSA.py on a single protein
> (not generated from a MD simulation).
>
> How does the mmpbsa.in (input file) and syntax MMPBSA.py -O .... look
> like,
>

You need to specify the structure using the '-y' flag of MMPBSA.py (you
still need the relevant topology files, though). Any file format that
cpptraj recognizes (PDB, mol2, mdcrd, netcdf, dcd, etc.) will work for
MMPBSA.py.

HTH,
Jason 

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
---------------------------------------------------------------------
*SECURITY/CONFIDENTIALITY WARNING:
This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p)
---------------------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 19 2012 - 15:30:03 PDT
Custom Search