What version of AmberTools are you using?
On Mon, Feb 27, 2017 at 12:52 PM, Vatsal Purohit
<vatsal.purohit15.gmail.com> wrote:
> Thanks for your suggestion Dan. Unfortunately, I got the error 'unknown
> flag: -c' when I tried that.
>
> -Vatsal
>
> On Mon, Feb 27, 2017 at 12:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Likely your restart file is in NetCDF format. Use the '-c' flag
>> instead of a redirect, e.g.
>>
>> $AMBERHOME/bin/ambpdb -p complex.top -c complex-init-md.rst >
>> complex-init-md.pdb
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Mon, Feb 27, 2017 at 12:29 PM, Vatsal Purohit
>> <vatsal.purohit15.gmail.com> wrote:
>> > Hello all,
>> >
>> > I am trying to convert an rst file to pdb after running a short md
>> > simulation and am getting the following error:
>> >
>> > ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 11374 0\
>> >
>> > I used the following program:
>> > $AMBERHOME/bin/ambpdb -p complex.top < complex-init-md.rst >
>> > complex-init-md.pdb
>> >
>> > and my .out file after the simulation looks fine so I'm not sure what's
>> > wrong with the rst.
>> >
>> > Kindly, advise.
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Feb 27 2017 - 10:30:03 PST
