[gmx-users] Re: rectify the charges

[Justin Lemkul]

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 <jalemkul at vt.edu>
> *To:* Arunima Shilpi <arunima.bioinformatics at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at 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

========================================