Hi Sammia,
I can see two errors within your tleap log.
To fix the 'FATAL: Atom .R<ALA 179>.A<HN 11> does not have a type.' errors you should remove all hydrogens within the 1geqc.pdb file. tleap uses a different naming schema for hydrogens and doesn't know how to interpret the atom type HN.
Now to fix your ligand problem I'd recommend two things. First rename both your mol2 to 3rg.mol2 and your frcmod file to 3rg.frcmod to keep them consistent with the name of the ligand within the pdb. Next you need open the 1geqc.pdb file and rename the ligand atoms to correspond with the atom names in the mol2 file.
For example:
ATOM 1944 C 3rg 1 34.953 10.803 72.827 -0.39 -0.00 .007 A
becomes
ATOM 1944 C1 3rg 1 34.953 10.803 72.827 -0.39 -0.00 .007 A
and
ATOM 1950 N 3rg 1 38.603 9.079 72.688 -0.34 -0.05 .264 N
becomes
ATOM 1950 N10 3rg 1 38.603 9.079 72.688 -0.34 -0.05 .264 N
Please know that my example is probably not correct, however be careful when doing this step as the atoms have to correspond exactly to their counterparts in the mol2 file or you'll get some very weird and incorrect simulation results. Also for clarity I often rename the HETATM records to ATOM records even for the ligand, however I don't know if this is required...
Best,
Parker
________________________________________
From: sammia khatak [saammia_kt.hotmail.com]
Sent: Friday, April 04, 2014 8:21 AM
To: amber.ambermd.org
Subject: [AMBER] new error
please help me in solving this problem i get same error each time i runtleap
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Received on Fri Apr 04 2014 - 06:00:05 PDT
