>> Using antechamber with the -rn flag does the trick. However, the manual
>> states that the default residue name is MOL if it is not present in the
>> input file. I didn't test this with another pdb but either this is a bug
>> or a wrong statement in the manual which should be fixed.
>
> I guess the manual is wrong, or being wrongly interpreted. Probably you
> are the first person to try to make a mol2 file with a blank residue
> field in the input pdb file.
The manual is wrong and I changed the lyx file.
The pdb file I used was generated by sander (the QM region of a QM/MM run). The residue name was printed in the wrong column, this is fixed now.
> Try making a prepin file and see what happens. The mol2 capability was added
> much later, and it could be that the option to handle a blank residue name
> was overlooked.
This works for a simple test. Default residue name is INT in this case. It fails, however, for the Zn complex.
All the best,
Andy
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Thu Jul 29 2010 - 14:00:04 PDT
