[gmx-users] error in converting charmm to gromacs

[Chanchal]

Hi Mark,
    I changed the capitalized words (CUTNB, CTOFNB, CTONNB, EPS, E14FAC,
WMIN) to lower case in the file par_all36_carb.prm and now when I executed
the command ./convert_charmm_to_gromacs.pl par_all36_carb.prm then I got no
error msg. When I created a topology file, I found that the 5th column
corresponding to dihedraltype is 9. But I guess it should be either 1 or 3.
I also found that the columns in ffcharmm*.itp are not aligned. Could this
be the reason?
Thanks
Chanchal

On Sun, Nov 22, 2009 at 10:12 AM, Chanchal <chanchal.kar at gmail.com> wrote:

> Hi Mark,
>    I need  36 because I am working with carbohydrate (mannose).  Here is
> the link for 36:
> http://mackerell.umaryland.edu/CHARMM_ff_params.html
> Plese look at this file: toppar_carbo_jul_2009.tgz<http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_carbo_jul_2009.tgz>
>
> It would be very helpful to me if you can fix the scripts accordingly.
> Thanks
> Chanchal
>
> On Fri, Nov 20, 2009 at 8:20 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>> Chanchal wrote:
>>
>>> Hi All,
>>>    I want to create ffcharmm*.itp file from par_all36_carb.prm using the
>>> script provided by Mark Abraham. While I used execute the command ./
>>> convert_charmm_to_gromacs.pl <http://convert_charmm_to_gromacs.pl>
>>> par_all36_carb.prm , I got this message:
>>> Argument "CTOFNB" isn't numeric in multiplication (*) at ./
>>> convert_charmm_to_gromacs.pl <http://convert_charmm_to_gromacs.pl> line
>>> 270, <GEN0> line 1382.
>>> Argument "EPS" isn't numeric in multiplication (*) at ./
>>> convert_charmm_to_gromacs.pl <http://convert_charmm_to_gromacs.pl> line
>>> 279, <GEN0> line 1382.
>>>
>>
>> As Justin said, you're giving inputs for which the script wasn't
>> developed, and the format could easily have changed. If you can tell me why
>> 36 is necessary and 27 insufficient for your needs, and a link to your
>> source for 36, then I'll look at why the 36 file doesn't work.
>>
>> Mark
>>
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>
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