VMD-L Mailing List

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Fri Sep 07 2012 - 09:41:54 CDT

Hi, the APBS feature in VMD appears to take either .psf paramterized or amber prmtop files as inputs and write the .pqr file needed for APBS calculation. This is remarkably easy for a single calculation, but I'm looking to automate calculations on a trajectory or every structure in an ensemble. I was wondering if this feature (converting a namd or amber parameterized file to .pqr) is available to the command line for scripting? Of for that matter, if any of the APBS functionality in VMD is available via the command line?

Thanks,
Erik

________________________________
Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer