Dear Jason,
Thanks for your reply.
Here are few lin how ligand entry look like in PDB, so here I have the
same name LIG both in library and PDB
ATOM 2402 C1 LIG 399 -5.832 206.865 113.746 1.00 0.00 C
ATOM 2403 C2 LIG 399 -5.592 207.397 112.468 1.00 0.00 C
ATOM 2404 C3 LIG 399 -7.096 206.469 114.088 1.00 0.00 C
ATOM 2405 C4 LIG 399 -8.120 206.606 113.137 1.00 0.00 C
ATOM 2406 C5 LIG 399 -7.838 207.138 111.860 1.00 0.00 C
ATOM 2407 C6 LIG 399 -6.554 207.543 111.517 1.00 0.00 C
Here is a selection of some lines from my library files
!!index array str
"LIG"
!entry.LIG.unit.atoms table str name str type int typex int resx
int flags int seq int elmnt dbl chg
"C1" "ca" 0 1 131072 1 6 -0.162000
"C2" "ca" 0 1 131072 2 6 -0.096000
"C3" "ca" 0 1 131072 3 6 -0.072500
"C4" "cp" 0 1 131072 4 6 -0.083800
"C5" "ca" 0 1 131072 5 6 0.005800
"C6" "ca" 0 1 131072 6 6 -0.159000
On 30 March 2010 18:51, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
>>>
>>> --
>>> ---------------------------------------
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Graduate Student
>>> 352-392-4032
>>>
>>> _______________________________________________
>>> AMBER mailing list
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Mar 30 2010 - 15:00:03 PDT
