Dear Amber users,
I am building a box of 3M Gdm HCl. I have already has built a box contains
48 molecules of Gdm but when I am trying to assign the charges using
antechamber (Amber 12)
./antechamber -i Gdm-48.pdb -fi pdb -o Gdm-48.mol2 -fo mol2 -c bcc -s 2
Unfortunately, I got
Warning: detected more than 10 Residue sequence numbers
Judge bond type for Residue 1 with ID of 1 and Name of Gdm ---
Info: Bond types are assigned for valence state 1 with penalty of 1
.
.
.
-Judge bond type for Residue 48 with ID of 48 and Name of Gdm ---
Info: Bond types are assigned for valence state 1 with penalty of 1
Running: /home/guest/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 1584; net charge: 0
Running: /home/guest/amber12/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/guest/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
bcc() in charge.c properly, exit.
So, i have to divide my pdb file into 4 pdb files containing 10 residues
and calculate charges and then recombine these files together or there are
more practical approaches.
best Regards,
said
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Received on Fri Feb 06 2015 - 08:00:03 PST
