Re: [AMBER] problem with antechamber for C60

From: Chun-Wei Pao <barbarossapao.gmail.com>
Date: Tue, 23 Mar 2010 22:44:19 +0800

Dear Raja

Thank you very much for your information. I tried to increased the PSCUTOFF to 10000 but the same error (see below) still occurred. Do you happen to have any idea how to solve this problem?

Error: cannot run "/home/barbarossapao/amber10/amber11/bin/bondtype -j full -i A
NTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() o
f antechamber.c properly, exit


C.W.

 
b 2010/3/23 U7:22 ɡA Raja Pandian gG

> Hi,
> This is not a major problem. You have to increase the PSCUTOFF (>100) on ANTECHAMBER and then recompile it.
> Because ANTECHAMBER has its own limit PSCUTOFF. So increase PSCUTOFF (>100) and then recompile it.
>
> On Tue, Mar 23, 2010 at 11:40 AM, Chun-Wei Pao <barbarossapao.gmail.com> wrote:
> Dear Amber users
>
> I am trying to use antechamber to generate GAFF parameters for simulation of
> C60 clusters. However, I found the following error:
>
> I key in
>
> $AMBERHOME/bin/antechamber -i fullerene2.pdb -fi pdb -o fullerene.mol2 -fo
> mol2 -c bcc
>
> and get
>
> 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 PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
>
> Error: cannot run "/home/cwpao/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
>
> Enclosed is the PDB file of the C60. Could anyone tell me what happened? I
> suspect that this is due to the pentagon C atoms.
>
> Thanks!
>
> C.W.
>
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>
>

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Received on Tue Mar 23 2010 - 08:00:06 PDT
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