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
>>
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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 - 11:00:04 PDT
