Re: AMBER: amber :antechamber problem

From: Florian Haberl <>
Date: Mon, 7 Jan 2008 17:33:02 +0100


On Saturday, 5. January 2008 04:51, jani sahil wrote:
> Hello amber user
> I got a problem when I try to produce ligand prep file using
> antechamber in AMBER8.0
> The following is what I did
> antechamber -i inb.pdb -fi pdb -o inb.prepin -fo prepi -c bcc -s 2
> the following error I got
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> I am attaching input file.
> Can anyone tell me how to deal with it? Thank you in advance.
> Best regard,

best thing is to use a file format with bond/atom information like mol2 files
(from sybyl or moe).
If you take ligands out of pdb files there is only the information of the
coordinates around, nothing more. Sometimes, e.g. not so good resolution of
the X Ray structure, causes bad input strucutres for antechamber.



 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT
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Received on Wed Jan 09 2008 - 06:07:16 PST
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