Dear Daniel
Thank you. I have run antechamber and have got Gdm.prepi file. Prepi file
0 0 2
This is a remark line
molecule.res
Gdm INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N1 nh M 3 2 1 1.540 111.208 -180.000 -0.516433
5 H11 hn E 4 3 2 1.000 43.383 -25.334 0.238367
6 H12 hn E 4 3 2 1.000 93.498 89.598 0.238367
7 C cz M 4 3 2 1.500 78.268 -161.170 0.298300
8 N3 nh B 7 4 3 1.500 109.483 -149.413 -0.500533
9 H31 hn E 8 7 4 1.000 109.518 -60.050 0.238367
10 H32 hn E 8 7 4 1.000 109.433 179.894 0.238367
11 N2 nh M 7 4 3 1.500 109.475 -29.346 -0.500533
12 H21 hn E 11 7 4 1.000 109.524 60.300 0.238367
13 H22 hn E 11 7 4 1.000 109.478 -179.686 0.238367
14 X 1 0 1 7.704 nan-10295.253 0.000000
LOOP
IMPROPER
N2 N1 C N3
DONE
STOP
Firstly, The chlorine ion disappeared. secondly, I do not know "What is
nan?".
Thirdly, When I ran parmchk, I got Segmentation fault (core dumped). I have
tried to add -p but I got the same massage. Why does this massage appear?
Please any suggestions would be appreciated.
Regards,
said
On Fri, Feb 6, 2015 at 6:23 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
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> > 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)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 06 2015 - 11:30:02 PST
