Hi there,
I have posted on the forum yesterday regarding an error on Antechamber but
I have only posted part of the error message:
Here is the whole error message:
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
increas
Error: cannot run "/app1/linux/amber10/bin/bondtype -j full -i
ANTECHAMBER_BOND_
of antechamber.c properly, exit
My project is to construct a series of alpha helices using GaussView and
run MD simulations in AMBER. During the conversion of Gaussian output file
into .mol2 I have ran into this error.
This was the command that I have used:
antechamber -i mol.log –fi gout –o mol.mol2 –fo mol2 –c resp -nc -2
Everything was fine for alpha helices containing most of the amino acid
residues so far except for Glutamic acid and Aspartic acid.
Thank you so much for your help.
Regards,
Ashley
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Received on Mon May 28 2012 - 21:30:02 PDT
