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 ¤U¤È7:22 ®É¡A Raja Pandian ¼g¨ì¡G
> 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.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 23 2010 - 08:00:06 PDT
