AMBER Archive (2005)

Subject: Re: AMBER: MM_PBSA help, please

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Mon Jul 11 2005 - 16:37:50 CDT

Armin,

That can work but it is tedious. I would use the commands suggested
at the top of http://amber.scripps.edu/bugfixes.html

namely,
% cp file_to_be_patched file.backup
% patch -c file_to_be_patched patchfile

On 7/11/05, opitz_at_che.udel.edu <opitz_at_che.udel.edu> wrote:
> Thank you! That did fix the problem. I have run into another problem. It
> appears that I need to implement Bugfix 7 for Amber 7.
> I'm fairly unexperienced with programming, so is it correct that I have
> to go into the mdread.f file and change the lines by hand?
>
> Best Regards,
>
> Armin
>
> ==============Original message text===============
> On Mon, 11 Jul 2005 14:30:34 EDT Scott Pendley wrote:
>
> Armin,
>
> I have seen that error when mm_pbsa is try to process snapshots and
> there are none available. As GC is marked zero, it assumes that you
> are not creating individual snapshots from a given trajectories. Is
> this what you wish to do?
>
> SURFTEN and SURFOFF are specific to the type of GB or PB that you are
> trying to perform. For a good referrence on this and mm_pbsa in
> general see "Converging Free Energy Estimates: MM-PB(GB)SA Studies on
> the Protein-Protein Complex Ras-Raf" Gohlke and Case. J Comput Chem
> 25:238-250 2004
>
>
>
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