Dear Jason,
I am sorry. By mistake the lower portions of file got deleted.
The problem is I am getting only 10 output pdb s from this script
where I should get 41 structures named 2b5e.new.pdb.1/.... 2b5e.new.pdb.41.
I am sorry I did not understand well what you mean by "it'll have
numbers appended to it".
Thanks a lot and would look forward to your reply.
Regards,
Moitrayee
> You didn't tell us what the problem was; only that there *was* a problem (in
> the subject of this email). There's no way we can diagnose a problem we
> know nothing about.
>
> This script should create a PDB file 2b5e.new.pdb.1, .2, .3, etc. It won't
> create a file with that exact name -- it'll have numbers appended to it.
>
> Good luck,
> Jason
>
> On Mon, Apr 11, 2011 at 9:20 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
>
>> Dear Amber Users,
>>
>> I am trying to write pdb files from CRD using the trajout command in Amber.
>>
>> The script is as follows:
>>
>> #!/bin/sh
>>
>> /soft/amber11/AmberTools/exe/ptraj 2b5e.prm.top << EOF
>>
>> trajin /media/USB_flash/PDI/CRD/2b5e.min1.crd
>> trajin /media/USB_flash/PDI/CRD/2b5e.0000_0010.crd
>> trajin /media/USB_flash/PDI/CRD/2b5e.0010_0020.crd
>> trajin /media/USB_flash/PDI/CRD/2b5e.0020_0030.crd
>> trajin /media/USB_flash/PDI/CRD/2b5e.0030_0040.crd
>>
>> trajout /media/USB_flash/PDI/PDB/2b5e.new.pdb PDB
>>
>> strip :WAT
>>
>> go
>>
>>
>>
>>
>>
>> --
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>> believed to be clean.
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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> believed to be clean.
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>
--
This message has been scanned for viruses and
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believed to be clean.
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Received on Mon Apr 11 2011 - 10:30:03 PDT
