[AMBER] Problem with antechamber/acdoctor

From: Sarah Fegan - UKRI STFC <sarah.fegan.stfc.ac.uk>
Date: Wed, 26 Sep 2018 10:15:11 +0000


I am trying to use AmberTools18 to create GAFF parameters for some small molecules. I started with the following antechamber command:

antechamber -i methyl-benzene.mol2 -fi mol2 -o methyl-benzene.ac -fo ac -c bcc -nc 0 -m 1 -df 2 -at gaff -du y -an y -j 4 -s 2 -eq 2 -rn LIG -ek "qm_theory='AM1',grms_tol=0.0002,tight_p_conv=1,scfconv=1.0d-10,itrmax=500,pseudo_diag=1,maxcyc=1000,"

This ran without producing any error messages. I then used the ac file output from antechamber as input to parmchk2 to create a frcmod file.

parmchk2 -i methyl-benzene.ac -f ac -o methyl-benzene.frcmod -a N

This command also ran without producing any error messages. However when I ran antechamber a second time using the ac file as input to get a mol2 file of the output (with the calculated charges), I got an error from acdoctor:

antechamber -i methyl-benzene.ac -fi ac -o output.mol2 -fo mol2 -s 2 -at gaff

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for ac File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded
      for those not bonded
   Status: pass
-- Check Weird Bonds --
/home/skfegan/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (1) for atom (ID: 1, Name: C1).
       Possible open valence.

Have I done something wrong, is there a problem with antechamber (something in bondtypes or atomtypes changing the molecule), or is it a problem with acdoctor? I should note this problem only seems to occur with aromatic molecules like methyl-benzene and there are no error messages with non-aromatic molecules like ethane. I am attaching the mol2, ac and frcmod files.

Any help you can give me would be appreciated.



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Received on Wed Sep 26 2018 - 03:30:02 PDT
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