AMBER Archive (2008)

Subject: Re: AMBER: stripping water from a restart file

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 23 2008 - 07:22:00 CDT

did you try generating the prmtop with leap as I sugggested before?

On Thu, Oct 23, 2008 at 7:33 AM, CHAMI F. <fatima.chami_at_durham.ac.uk> wrote:
>
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu on behalf of Bill Ross
> Sent: Wed 22/10/2008 21:38
> To: amber_at_scripps.edu
> Subject: RE: AMBER: stripping water from a restart file
>
>> What error msg was given?
>>
>> Unit 30 Error on OPEN: dimer-vac_md.rst_1000000=20
>
> That unit number looks fishy. What args did you run sander with?
>
> $AMBERHOME/exe/sander.MPI -O -i mdin -p dimer.prmtop -c
> dimer-vac_md.rst_1000000 -r jar_1.rst -o jar_1.out -x jar_1.mdcrd
>
> I suspect that the topology file generated after stripping water using
> rdparm is different form the topology file generated by Leap
>
> fatima
>
>
> Bill
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