Again I will remind you to keep all Gromacs-related correspondence on the
gmx-users list. I am CC'ing the list and expect that all future questions and
discussion will be posted there.
On 2/5/13 9:52 PM, Arunima Shilpi wrote:
Hello sir
I would like to know how do we rectify the charges of the atom in .itp file. I
did refer the manual but was unsuccessful . Here I am forwarding you the .itp
file file.
The manual does not contain how-to information for dealing with all possible
force fields. You will have to spend considerable time in the literature
reading about the force field you have chosen, how it was derived, and how you
can extend it with some arbitrary molecule.
Without context, there is little to suggest. It appears the output below is
from PRODRG and thus you are dealing with some parameter set within the Gromos96
force field family. Consider the following:
http://pubs.acs.org/doi/abs/10.1021/ci100335w
-Justin
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 DRG OXT 1 -0.704 15.9994
2 C 1 DRG C 1 0.390 12.0110
3 OM 1 DRG O 1 -0.704 15.9994
4 CH1 1 DRG CA 1 0.172 13.0190
5 NL 1 DRG N 1 0.694 14.0067
6 H 1 DRG H3 1 0.004 1.0080
7 H 1 DRG H4 1 0.004 1.0080
8 H 1 DRG H1 1 0.004 1.0080
9 CH2 1 DRG CB 1 0.140 14.0270
10 CH2 1 DRG CAT 2 -0.010 14.0270
11 S 1 DRG SAS 2 0.010 32.0600
12 CH2 1 DRG CAR 3 0.107 14.0270
13 CH1 1 DRG CAE 3 0.206 13.0190
14 OA 1 DRG OAD 3 -0.214 15.9994
15 CH1 1 DRG CAA 3 0.134 13.0190
16 OA 1 DRG OAG 3 -0.225 15.9994
17 H 1 DRG HAG 3 0.041 1.0080
18 CH1 1 DRG CAB 3 0.134 13.0190
19 OA 1 DRG OAF 3 -0.225 15.9994
20 H 1 DRG HAF 3 0.042 1.0080
21 CH1 1 DRG CAC 4 0.487 13.0190
22 NR 1 DRG N9 4 0.461 14.0067
23 CR1 1 DRG C8 4 -0.003 12.0110
24 HC 1 DRG H8 4 0.055 1.0080
25 NR 1 DRG N7 5 -0.541 14.0067
26 C 1 DRG C5 5 0.127 12.0110
27 C 1 DRG C4 5 0.252 12.0110
28 NR 1 DRG N3 5 -0.556 14.0067
29 CR1 1 DRG C2 5 -0.004 12.0110
30 HC 1 DRG H2 5 0.026 1.0080
31 NR 1 DRG N1 5 -0.556 14.0067
32 C 1 DRG C6 5 0.252 12.0110
33 NT 1 DRG N6 6 0.000 14.0067
34 H 1 DRG H62 6 0.000 1.0080
35 H 1 DRG H61 6 0.000 1.0080
--------------------------------------------------------------------------------
*From:* Justin Lemkul <jalem...@vt.edu>
*To:* Arunima Shilpi <arunima.bioinformat...@yahoo.com>; Discussion list for
GROMACS users <gmx-users@gromacs.org>
*Sent:* Tuesday, 5 February 2013 9:15 PM
*Subject:* Re: [gmx-users] error in running command
On 2/5/13 9:04 AM, Arunima Shilpi wrote:
> Dear Sir/ Madam
>
> I am using gromacs for simulation and has the following while running the
command for "grompp"
> Expected integer argument for option -maxwarn "".
>
> I do not want use maxwarn to bypass the error.
>
> I request you to kindly help me out to debug the error.
If you don't want to use -maxwarn, then omit it from your command.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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