Hi,
The 'antechamber' program is designed to develop parameters for a
single residue only. What you want to do is generate parameters for a
single Gdm residue, which can then be used with leap to create a
topology file for systems containing multiple Gdm residues.
-Dan
On Fri, Feb 6, 2015 at 8:54 AM, Ibrahim Said <saidibrahim569.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 06 2015 - 08:30:02 PST
