RE: [AMBER] minimization with pmemd and gbsa=1

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 21 May 2010 07:20:48 -0700

Hi Paul

> Does pmemd10 support minimization with GB solvation? I'm hoping to use
> the
> patch for cuda support and do my minimizations on a gpu.

Yes but not with gbsa=1. You need to turn off the surface area calculations.
I would NOT advise using the patch against AMBER 10 though, it has not been
thoroughly tested and is no longer supported / updated. I would suggest
switching to the PMEMD in AMBER v11.

All the best
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |

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Received on Fri May 21 2010 - 07:30:04 PDT
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