Dear Ramesh,
It seems like the problem is due the ions in your pdb file. Apparently
the residue index for both Cl and Na is 1, the same as first DOPC
molecule (I don't know why this happens). That's why I got the error
Konsole output
Error: Number of atoms in residue does not match number of atoms in
residue in replacement data file
from charmmlipid2amber. When I changed the residue indexes of Na and Cl
to 144 and 145, respectively, charmmlipid2amber worked correctly.
Best,
Batuhan
On 04/15/16 14:16, Shreeramesh wrote:
> Dear Sir,
>
> Thanks for your reply. The problem is at charmmlipid2amber step and the
> output file was not generated for the following command.
>
> $ charmmlipid2amber.py –i rec.pdb [-c substitution_definitions.csv] \ -o
> rec2.pdb
>
>
> The system shows the following message without showing any error
>
> Usage: charmmlipid2amber.py [-c charmmlipid2amber.csv] -i input.pdb -o
> output.pdb
>
>
> Thanks & regards
>
> *Dr. Ramesh M*
> Email: shreeramesh.gmail.com
> Mobile: (91) + 9646469938 (27) + (0) 844556164
>
> On Fri, Apr 15, 2016 at 5:03 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Fri, Apr 15, 2016, Shreeramesh wrote:
>>> I use the following script for the conversion and was unsuccessful.
>> It would be most helpful if you could indicate what the symptoms of the
>> problem are. It's not even clear (at least to me) whether the error was
>> in the charmmlipid2amber step or the tleap step.
>>
>> ...thx...dac
>>
>>
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Received on Fri Apr 15 2016 - 05:30:08 PDT
