Thank you.
I tried just making a mol2 file, and got the same error. With command:
antechamber -i retch.pdb -fi pdb -o retch.mol2 -fo mol2 -c bcc
The error was:
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
Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/usr/local/amber/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit
Attached is the retch.pdb file that I used.
I got the same error when trying to use this pdb file, and previously when I was just using a gaussian log file.
Anything I did wrong?
Thanks
Mark
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of case [case.biomaps.rutgers.edu]
Sent: Saturday, December 19, 2009 12:33 PM
To: AMBER Mailing List
Subject: Re: [AMBER] antechamber bond type error
On Fri, Dec 18, 2009, Mark M Huntress wrote:
> Hi, I am trying to parameterize a molecule (protonated, positively
> charged retinal) and I am getting the following error when I put in the
> following input:
I'm not sure we can help much without seeing your input files. But try this:
does your molecule run OK in the more "standard" of having a pdb file as
input, and mol2 as output (with either no charges or bcc charges)?
That would help see if the problem is in parsing the rt.log file; also, if you
post a pdb file, users on the list can more easily see if they spot any
problems.
...dac
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Received on Tue Jan 05 2010 - 16:30:02 PST
