Dear Dr. Jason, Dr. case,
Thank you very much for your help.
There was difference in name of ligand. Library had the name DXQ whereas PDB
had it as LIG. I changed pdb files to match the name.
It is working well now.
Thank you
Regards,
On Thu, Jul 22, 2010 at 12:10 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> A slight modification to Professor Case's statement. In this case, you
> made an off library, so he residue name in DXQ.lib or whatever you called it
> must be the same as that residue's name in the pdb you're loading. It looks
> like it's called LIG in the pdb, but not in the off file. You can just
> change the residue name in the pdb to match the library for each atom in
> that residue.
>
> Hope this helps,
> Jason
>
> --
> Jason Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> On Jul 21, 2010, at 9:09 AM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Wed, Jul 21, 2010, kamlesh sahu wrote:
> >>
> >> I am using amber 10 to simulate small molecules (modified a little as
> >> compared to original pdb structure). First I used antechamber to fit
> ligand
> >> parameters and then I used tleap to generate library in this way -
> >> ~/src/Xtruct/trunk/amber_10_install/bin/antechamber -i DXQ-11_h.pdb -fi
> pdb
> >> -o DXQ-11.mol2 -fo mol2 -c bcc -s 2 -j 5 -nc +2
> >>
> >>
> >> It gives error messages -
> >>
> >> FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
> >
> > This generally means that atom or residue names in the pdb file don't
> match
> > those in the DXQ-11.mol2 file you created above. You have to make them
> > exactly match, and the names are case-sensitive.
> >
> > Also, study the leap.log file carefully: there should be other messages
> > pointing out the problem, especially if my diagnosis is correct.
> >
> > ....dac
> >
> >
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--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Wed Jul 21 2010 - 20:30:03 PDT
