This may still be the answer:
http://archive.ambermd.org/201311/0151.html
Bill
On 2/27/17 9:52 AM, Vatsal Purohit 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.
>>> _______________________________________________
>>> AMBER mailing list
>>> 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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Received on Mon Feb 27 2017 - 10:30:02 PST
