Hi have installed just Ambertools 1.4 and I am working on paramerization
of acetyl-Coa from 3PW8. However there are some problem since I am
unable to applies calcluate the right charge either using bcc or gas
with antechamber. I have followed the
http://ambermd.org/tutorials/basic/tutorial4b and read the manula
regarding antechamber. When I do run antechamber i got this results.
[knutjbj. 3PW8]$ antechamber -i ACOh.pdb -fi pdb -o aco.mol2 -fo mol2 -c
bcc -s 2 -j 5 -nc 0
Running: /home/knutjbj/amber/amber10/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
For atom[26]:O2A, the best APS is not zero, bonds involved by this atom
are frozen
For atom[30]:O5A, the best APS is not zero, bonds involved by this atom
are frozen
For atom[39]:O9P, the best APS is not zero, bonds involved by this atom
are frozen
For atom[44]:O5P, the best APS is not zero, bonds involved by this atom
are frozen
For atom[50]:O, the best APS is not zero, bonds involved by this atom
are frozen
Running: /home/knutjbj/amber/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 418; net charge: 0
Running: /home/knutjbj/amber/amber10/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/knutjbj/amber/amber10/bin/sqm -O -i sqm.in -o
sqm.out" of bcc() in charge.c properly, exit
It seem that is is unable to converge after 1000 steps. Is there any way
to increase the number of step or should I chose another method to
calculate charge? I have used Pymol to extract the acetyl-coa.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 12 2011 - 10:30:04 PST
