Hi there,
I am using AT 1.3 (with sqm) in either Linux 64 (Debian 5.0 with gcc) and
Mac OSX (10.6.2 with intel and intel mkl).
I am trying acpypi (among other things, a python wrapper for antechamber)
on Bej.none_neutral.ideal.mol2 (in attach), from
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=BEJ&PARENTINDEX=-1&APPLICATION=1
I did:
/usr/local/amber11/bin/antechamber -i Bej.none_neutral.ideal.mol2 -fi mol2
-o Bej.none_neutral.ideal_bcc_gaff.mol2 -fo mol2 -c bcc -nc 0 -m 1 -s 2 -df
2 -at gaff -pf n # may take more than an hour to run
/usr/local/bin/parmchk -i Bej.none_neutral.ideal_bcc_gaff.mol2 -f mol2 -o
Bej.none_neutral.ideal_AC.frcmod
/usr/local/bin/tleap -f tleap.in
where tleap.in is:
verbosity 1
source leaprc.ff99SB
source leaprc.gaff
mods = loadamberparams Bej.none_neutral.ideal_AC.frcmod
BEJ = loadmol2 Bej.none_neutral.ideal_bcc_gaff.mol2
check BEJ
saveamberparm BEJ Bej.none_neutral.ideal_AC.prmtop
Bej.none_neutral.ideal_AC.inpcrd
saveoff BEJ Bej.none_neutral.ideal_AC.lib
quit
The problem is that if run such commands in my Mac, the final net charge is
0.004 and tleap: check BEJ doesn't complain.
But if I run on linux, net charge is 0.01 and then tleap prints:
Checking 'BEJ'....
ERROR: The unperturbed charge of the unit: 0.010000 is not integral.
WARNING: The unperturbed charge of the unit: 0.010000 is not zero.
Checking parameters for unit 'BEJ'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 1 Warnings: 1
The charges are calculated by antechamber and showed
in Bej.none_neutral.ideal_bcc_gaff.mol2, and I can see them in
ANTECHAMBER_AM1BCC.AC.
Which leads me to a long lasting question: why the am1bcc charges are not
properly balanced in the very beginning?
And then it seems to me that tleap check has a tolerance, probably set in
its code, what would it be?
Many thanks in advance,
Alan
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 12 2010 - 06:00:02 PST
