[AMBER] Problems with tetrahedral Al in antechamber

From: Gonzalo Jimenez <gonzalojimenezoses.gmail.com>
Date: Mon, 19 Mar 2012 01:44:19 -0700

Dear all,

I am trying to calculate the RESP charges using the standard protocol with Antechamber in Amber 11 AT1.5. The molecule is an organometallic compound with two tetrahedral Al atoms.
When running antechamber:

antechamber -i DOSY_base_b3lyp.log -fi gout -o DOSY_base_b3lyp.prepin -fo prepi -c resp -at gaff

the following error appears:

For atom[15]:Al1, the best APS is not zero, bonds involved by this atom are frozen

For atom[47]:Al2, the best APS is not zero, bonds involved by this atom are frozen

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 "/u/local/apps/amber/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit

Is there any quick solution for this problem?

Thanks a lot,
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Received on Mon Mar 19 2012 - 02:00:04 PDT
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