AMBER Archive (2003)

Subject: Re: Max residues (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Fri Mar 07 2003 - 11:12:29 CST

---------- Forwarded message ----------
Date: Wed, 5 Mar 2003 11:04:53 -0800
From: David A. Case <case_at_scripps.edu>
Reply-To: amber_at_heimdal.compchem.ucsf.edu
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: Max residues (fwd)

On Wed, Mar 05, 2003, amber_at_heimdal.compchem.ucsf.edu wrote:
>
>
> Are the maximum number of residues that leap can read in set at 10,000 and
> if so how does one go about increasing this number???
>
> I have created a protein bilayer simulation cell (pdb file), with quite a
> large number of water molecules. The number of residues appears to be too
> much for leap which deletes some of the water molecules present leaving a
> total of 10000 residues in the resulting saved pdb file.

I think it should work if you can write a script to start the residue
numbering over again at 1 once you get to 10,000 residues. I don't know
what you pdb file looks like for the large residue numbers, but the above
trick should work. Basically, LEaP looks to see if the residue number has
changed in order to decide when to create a new residue.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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