Re: [AMBER] Simulation of complex

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Date: Wed, 21 Apr 2010 05:24:12 -0400 (EDT)


> 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.

>From a look at your pdb, all atoms in MOL have names like C, N and H.
Unfortunately, amber assigns everything by atom name, so the names in your
pdb file have to be unique (C1, C2, N3...) and they have to exactly match
the atom names in your prepin file (which are autogenerated by amber).
Just having the right atom order is not going to help you in leap.

So you should change all the atom names of MOL in your pdb to match the
corresponding names in your ligand prepin, then load those into leap.

Unfortunately this sort of renaming is quite common when adapting docking
results for amber.

Kind Regards,


> The complete leap.log is attached along with all the files that are
> mentioned.
> 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,
> Bangalore-560012
> _______________________________________________
> AMBER mailing list

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Apr 21 2010 - 02:30:08 PDT
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