From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Sep 24 2015 - 07:37:04 CDT
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..
On Thu, Sep 24, 2015 at 5:43 PM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
> 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 <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Neelanjana Sengupta <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
> 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
> Thanks in advance.
-- ~~~~~~~~~~~~~~~~~~~~ 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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