Sorry, I should have asked you this before; what version of Amber are
you using and what bugfixes have been applied?
The getcor routine is use to read coordinate files, so perhaps there
is an issue with the file? Could you send me (off-list) the
2am9_mb_ini.prmtop and md_cpeq4nowat.restrt files so I can check them?
Thanks.
-Dan
On Wed, Jul 25, 2012 at 10:09 AM, Shafinaz Chowdhury
<Shafinaz.Chowdhury.bri.nrc.ca> wrote:
> Dear Dr. Roe
>
> I tried it again with your advice.
>
> Command line I used
>
> sander -O -i SASA1.in -p 2am9_mb_ini.prmtop -c md_cpeq4nowat.restrt -y
> 2am9_mdwild.trj -o SASA1.out
>
>
> Here, md_cpeq4nowat.restrt is restrt file used for md production run after
> pressure equlibration step. Still I got eh same message.
>
> At line 225 of file _getcor.f
> Fortran runtime error: Bad value during integer read
>
> I really appreciate if can help me.
>
> Waiting for your reply.
>
> Shafinaz
>
>
> -----Original Message-----
> From: Shafinaz Chowdhury [mailto:Shafinaz.Chowdhury.bri.nrc.ca]
> Sent: Tuesday, July 24, 2012 4:41 PM
> To: 'amber.ambermd.org'
> Subject: Re: [AMBER] How to Calculate SASA with Amber?
>
>
> Dear Dr. Roe
>
> I used following input file to calculate SASA of individual snapshots of a
> trajectory named 2am9_mdwild.trj and its prmtop file name is
> 2amp_amb_ini.prmtop.
> Input file SASA1.in
>
> #SASA energy evaluation of the trajectory
> &cntrl
> imin=5,igb=5, gbsa=2,
> ntx=1, maxcyc=0,
> ntc=1, ntf=1,
> ntb=0, ntp=0,
> surften=1,
> ntwe=0, ntpr=500, ntwx=1,
> cut=1000,
> &end
>
> Comand line I used is
>
> sander -O -i SASA1.in -p 2am9_mb_ini.prmtop -c 2am9_mdwild.trj -o SASA1.out
>
> I got an error message
>
>
> At line 225 of file _getcor.f
> Fortran runtime error: Bad value during integer read
> Could you please help me in this regard.
>
> I really apprecaite your help.
>
> Regards.
>
> Shafinaz Chowdhury,PhD
> Computational chemist
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jul 25 2012 - 09:30:06 PDT
