[AMBER] antechamber is failing for a molecule

From: Alan Wilter Sousa da Silva <awilter.ebi.ac.uk>
Date: Wed, 19 Jan 2011 11:30:04 +0000

Hi there,

I am trying to run antechamber for an specific mol and I am getting this
error:

antechamber -i TB11_noprot.pdb -fi pdb -o TB11_noprot_bcc_gaff.mol2 -fo mol2
-c bcc -nc -2 -m 1 -s 2 -df 0 -at gaff -pf n
Running: /Users/alan/Programmes/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

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 "/Users/alan/Programmes/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit

If running the protonated version of the mol with -nc -1 all goes fine.

The pdb files are attached.

Any help would be appreciated, many thanks in advance.

Alan

-- 
Alan Wilter SOUSA da SILVA, D.Sc.
Bioinformatician, UniProt - PANDA, EBI-EMBL
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588




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Received on Wed Jan 19 2011 - 04:00:03 PST
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