AMBER Archive (2009)

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

From: Maria Mirza (maryamirza_at_gmail.com)
Date: Tue Aug 25 2009 - 00:17:59 CDT

Thanks Ross. Your initial answer to my previous question actually solved
both the problems. I was not aware of the renumbering going on as prmtop
files were generated if the original pdb did not start at 1, so everything
was shifted by 1.
Generating the pdb from parmtop helped visualize and solve both issues that
had taken me a week.

Thanks again for the quick response! I appreciate it.

On Tue, Aug 25, 2009 at 1:00 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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-- 
Only 'No Differences' can make a difference.
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