Can you send your files so that we can take a look?
On Tue, Mar 30, 2010 at 1:50 PM, imtiaz shafiq <imtiazshafiq.gmail.com> wrote:
> Dear Jason,
>
> No my original PDB file and library file both have a same name and
> that is LIG which correspond to my ligand. I am not sure why tleap is
> saving it as a MOL.
>
> Regards
> Imtiaz
>
> On 30 March 2010 18:45, Jason Swails <jason.swails.gmail.com> wrote:
>> Hello,
>>
>> What does your .lib file look like?
>>
>> Does it say "MOL" in there?
>>
>> All the best,
>> Jason
>>
>> On Tue, Mar 30, 2010 at 1:43 PM, imtiaz shafiq <imtiazshafiq.gmail.com> wrote:
>>> Dear All,
>>>
>>> I have a protein with an organic ligand. I have the force field
>>> parameters (.frcmod) and .lib files for the ligand. I can easily creat
>>> the prmtop and inpcrd files for this complex. Now my question is when
>>> I use savepdb command in tleap to save this complex I have noticed
>>> that the residue name for ligand change to MOL. I have tried with an
>>> other ligand and found a similar thing that the ligand name change to
>>> MOL.
>>>
>>> Further analysis of prmtop file also indicated that it also have a MOL
>>> entry. Please help me how I can keep the original name of the ligand
>>> when saving a PDB file with savepdb command or I have to manually
>>> change it every time.
>>>
>>> Regards
>>> Imtiaz
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> ---------------------------------------
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 30 2010 - 11:00:05 PDT
