Re: Solvation free energy calculation with MM/GBSA

From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Thu Sep 24 2015 - 07:40:43 CDT

yes, you have to make sure the commands and the top and parameter files you used in namd, including the one you used in modelling your structure. It is straight forward, further, you may load them to vmd and analyse again. Had used this method previously. You need to have large number of trajectories for gobs method.

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

________________________________
From: Neelanjana Sengupta <senguptan_at_gmail.com>
Sent: Thursday, September 24, 2015 8:37 PM
To: Abhishek TYAGI
Cc: NAMD
Subject: Re: namd-l: Solvation free energy calculation with MM/GBSA

Dear Abhishek,

Thanks for the reply. Is it straightforward to use chamber when their are non-standard topologies involved (particularly those that have been created manually)? Would appreciate your sharing your experience..

Regards,
Neelanjana

On Thu, Sep 24, 2015 at 5:43 PM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk<mailto:atyagiaa_at_connect.ust.hk>> wrote:

Dear Neelanjana,

if you want to use AMBER GBSA method, its easy you need to follow their tutorial and modify your files accordingly, you need to convert the par and top file including sf pdb file to their format, this may not that accurate as we follow charm ff in NAMD, and when it converts to AMBER format it may some issues and dcd files will be used directly as input for trajectories. Although, they claim its OK.

You need to use chamber available in amber tool, freely available followed by mm-gbsa calculations for quasi harmonic approximation.

Further, you may check their mailing list and this issue was discussed several times over their.

Best wishes

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

________________________________
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of Neelanjana Sengupta <senguptan_at_gmail.com<mailto:senguptan_at_gmail.com>>
Sent: Wednesday, September 23, 2015 7:51 PM
To: NAMD
Subject: namd-l: Solvation free energy calculation with MM/GBSA

Dear NAMD community,

We would like to calculate the solvation free energy, using the Generalised Born Surface Area (MM-GBSA) method, of a protein-nanosurface system that has been simulated with NAMD; we have the PSF file and the DCD files.

Could you suggest how to go about this? (The APBS method will only allow the PBSA method).

We are investigating options where we convert our trajectories to the AMBER format and use the utilities available there, but this is very messy...

Thanks in advance.

Regards,
Neelanjana

--
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Neelanjana Sengupta, PhD
Physical Chemistry Division
National Chemical Laboratory
Dr. Homi Bhaba Road
Pune 411008, India
Phone: +91-20-2590 2087
Fax: +91-20-2590 2636
URL:  http://academic.ncl.res.in/n.sengupta
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