AMBER Archive (2008)

Subject: Re: AMBER: mmpbsa INSTRNG error?

From: Gohlke_at_bioinformatik.uni-frankfurt.de
Date: Sun Mar 09 2008 - 11:13:05 CDT


Dear Sergio,

> It never finds a "SALT" key, so istrng is always 0. By looking into
> the mm_pbsa_input.pm file, it seems like the key should be "ISTRNG"
> instead of "SALT". So, if I rewrite this, I get what I think is the
> desired input in the pbsa.in file. Is this correct? or is the
> orignal code correct?

Your suggestion is correct. The SALT key originated from the delphi
keyword, whereas the ISTRNG key came with the introduction of Amber's
pbsa. If you replace SALT with ISTRNG in mm_pbsa_calceneent.pm,
..._createinput.pm, and ..._readinput.pm you should be fine.

Best regards

Holger

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