From: Klas Karis (karis.klas_at_gmail.com)
Date: Thu Jul 10 2014 - 12:11:35 CDT
Hi Fotis,
I know about those files. They do not include the martini polarizable
water though, which is what I want.
/Klas
2014-07-10 4:17 GMT-05:00 Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr>:
> Hello Klas,
>
> You can find the MARTINI topology and parameter files for protein, lipids,
> ions, water etc in the RBCG tutorial files:
> http://www.ks.uiuc.edu/Training/Tutorials/martini/files.tar.gz
> All MARTINI Material is located in the '04-cgc-top-par-files' folder. They
> are all in CHARMM format.
> Someone (i.e. the web admins) should, at some point, make a more official
> page in the site for these parameters.
>
> Cheers,
> Fotis Baltoumas
>
>
>> Hi NAMD users,
>>
>> Considering the time that have passed since the Martini polarizable
>> water first was published, which is about 4 years [1], I'm a little
>> bit surprised to find essentially nothing about where to find
>> parameter or topology files for use in NAMD/VMD when searching the web
>> and scrolling through the NAMD and VMD mailing lists.
>>
>>
>> My question is if anyone can point to where I could find
>> topology/parameter files for the martini polarizable water (in charmm
>> format), if they are publicly available.
>>
>>
>> I know it is not many lines to write my own topology and parameter
>> files, but I think, for future reference, there should be at least one
>> post in the mailing list telling either where to find the files if
>> they are publicly available or it's so simple that anyone interested
>> should write the files themselves.
>>
>>
>>
>> [1] S.O. Yesylevskyy et al. "Polarizable water model for the
>> coarse-grained Martini force field." PLoS Comp. Biol, 2010
>>
>>
>> Thanks!
>>
>> --
>> Klas Karis
>>
>>
>
>
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