[gmx-users] Cholesterol parameters (Charrm36) in GMX

[David van der Spoel]

On 2012-11-01 09:47, Yorquant Wang wrote:
> Hi David:
>      I have tested the script.  The input are 1 charmm topology file,
> 2 corresponding charmm parameter file and 3 foldername. But there are a
> lots of "top_all***.rtf" files and "par_all***.prm" files in
> "toppar_c36_aug12/toppar" folder, I don't know which pair is the correct
> pair. Could you give me a clue?
>      The new parameter for cholesterol is stored in "chol_new.str". If it is
> OK that I just put "chol_new.str" into the "toppar_c36_aug12/toppar/"
> folder and transfer it directly.
>
Don't know. I think you  need everything gromacs related that comes out.

Do it in an empty directory.

>      Thank you for replying!
> yorquant
>
>
> 2012/11/1 David van der Spoel <spoel at xray.bmc.uu.se>
>
>> On 2012-10-31 16:31, Yorquant Wang wrote:
>>
>>> Hi GMX-users,
>>>
>>>
>>> Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently
>>> provided Cholesterol parameters for Charmm FF.  Does anyone  have the
>>> corresponding .itp file for cholesterol in GMX style?
>>>
>>> Thanks for replying,
>>>
>>> Yukun
>>>
>>>   there's a script charmm2gromacs-pvm.py on the gromacs website that you
>> can download. Use with care.
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se