[AMBER] Problem with running antechamber on a small molecule

From: Devlina Chakravarty <devlina.chakravarty.gmail.com>
Date: Mon, 5 Dec 2011 16:23:36 +0530


I am trying to run antechamber on a small molecule,
S-ADENOSYLMETHIONINE, in order to create the parameter files. When I
tried using the original pdb file, there was a problem with
connectivity. So I tried using the PRODRG server to create a pdb file
with Hydrogen added. Now I am facing a different problem. I have
pasted the error message which I am getting while running antechamber
below. I have also attached the pdb file I am using and the mopac.out
file, since there is some problem in finding charges in the mopac.out
I would be very obliged if there could be any solution to this issue.

$ antechamber -i SAM-H-prodrg.pdb -fi pdb -o sam.prep -fo prepi -c bcc

Info: Bond types are assigned for valence state 3 with penalty of 1

Total number of electrons: 211; net charge: 0
INFO: Number of electrons is odd: 211
      Please check the total charge (-nc flag) and spin multiplicity (-m flag)

Running: /software/amber10/bin/mopac.sh
Error: unable to find mopac charges in mopac.out

Thanks in advance,
Devlina Chakravarty
Bose Institute

AMBER mailing list

Received on Mon Dec 05 2011 - 03:00:03 PST
Custom Search