AMBER Archive (2009)

Subject: RE: [AMBER] sander does not print out all residues in range.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Aug 25 2009 - 00:00:03 CDT

Hi Maria,

Are you certain there are 270 residues in your system? Note sometimes pdb
files are missing certain residues. E.g. your original pdb file may be
missing residue 1 such that the residue numbering starts at 2. When Leap
reads the pdb it numbers the residues sequentially so residue 2 in the pdb
would become residue 1 etc giving you a total of 269 residues in your
system. You can check this by running the prmtop file through rdparm and
entering the command parminfo.

You should also check your output file to see what sander actually reported
that it recognized during the initial startup.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Maria Mirza
> Sent: Monday, August 24, 2009 9:33 PM
> To: AMBER Mailing List
> Subject: [AMBER] sander does not print out all residues in range.
>
> Hello ,
>
> I am running sander using the following input file
>
>
> &cntrl
> ntf = 1, ntb = 0, dielc = 1.0,
> idecomp= 4,
> igb = 2, saltcon= 0.00,
> offset = 0.09,
> intdiel= 1.0, extdiel= 80.0,
> gbsa = 2, surften= 1.0,
> cut = 999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
>
> imin = 1, maxcyc = 1, ncyc = 0,
> &end
> Residues considered as REC
> RRES 2 270
> END
> Residues to print
> RES 2 270
> END
> END
>
>
> However, the output ONLY contains the records for residues 2-269 and
> nothing
> for 270. Residues 270 is a drug bound to this receptor. I just dont
> understand what's happening.
> There are no error messages or warnings in the output.
>
> The command used is
>
> sander -O -i sander.in -o sander_com.out -p complex.prmtop -c
> complex.crd
>
> Any suggestions?
>
> Maria
> --
> Only 'No Differences' can make a difference.
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