[AMBER] Simulation of complex

From: Asfa Ali <asfa.iisc.gmail.com>
Date: Wed, 21 Apr 2010 12:49:23 +0530


I am sorry to give less details. The detailed procedure which I followed is
as follows:

I docked my ligand to DNA using Autodock4 and saved the stablest complex as
pdb file (2hy9-l1-com.pdb). I took the ligand information from the complex
pdb and saved it as lig.pdb (prp-coot.pdb). Then I gave the ligand pdb in
Gaussian for resp charge calculation using

#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) fopt

which gave a gaussian output file (prpcoot.log).

Then the following commands were used:

antechamber -i prpcoot.log -fi gout -o prp.prepin -fo prepi -c resp
---no error (gave prp.prepin)

parmchk -i prpcoot.prepin -f prepi -o prp.frcmod
--no error (gave prp.frcmod)

Now I have modified the ligand name from LIG to MOL in 2hy9-l1-com.pdb and
named it as 2hy9-complex.pdb.

However how do I give the atom types for ligand in 2hy9-complex.pdb? The
ligand atom names are same but how do I fix it?

Now with this, if I proceed to tleap, following occurs:

WARNING: The unperturbed charge of the unit: -20.999998 is not zero.
FATAL: Atom .R<MOL 27>.A<C 91> does not have a type.
FATAL: Atom .R<MOL 27>.A<N 92> does not have a type.
FATAL: Atom .R<MOL 27>.A<H 93> does not have a type.
Failed to generate parameters
Parameter file was not saved.

The complete leap.log is attached along with all the files that are

I tried a lot but could not solve. Please help me..

Asfa Ali.

Prof. Santanu Bhattacharya's group,
Dept. of Organic Chemistry,
Indian Institute of Science,

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Received on Wed Apr 21 2010 - 00:30:03 PDT
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