VMD-L Mailing List

From: RAHUL SURESH (drrahulsuresh_at_gmail.com)
Date: Sat Dec 16 2017 - 00:12:31 CST

Thank you all..

few points to be sorted out.

1. I tried working with the tool and generated structure.top file but it
doesnt exactly look like the one which is generated using gromacs.

2. How can I generate gro file?

3. Here, itp file becomes a mandatory one to be added in protein.top file
for gromacs simulations.

On Fri, Dec 15, 2017 at 11:55 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Yeah. Mailing lists don't like NREL emails. :( John knows, and there are
> ways of fixing it, I'm just not sure if it has been implemented yet. One
> note: if you are using 1.9.3, the procedure will error for you due to a
> mistake introduced right before release. The beta builds of 1.9.4 will
> work, as will 1.9.2, or commenting out the offending line within the
> plugins directory of 1.9.3 (see the discussion in a previous entry to the
> list: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28199.html).
> ParmEd will work too. Neither approach will get you an itp file, but those
> aren't strictly speaking needed for most simulation applications.
>
> -Josh
>
> On 12/15/2017 09:02 AM, Giacomo Fiorin wrote:
> For some reason Josh Vermaas' messages to the list are occasionally
> filtered out by anti-spam filters, so I'll paste here what would be quite
> useful in your case:
> http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00103
> ://na01.safelinks.protection.outlook.com/?url=http%3A%2F%
> 2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Facs.jcim.6b00103&
> data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Ca9b6e93a8bb14298485f08d543d5
> 48a5%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%
> 7C636489505697944503&sdata=jTeg20SOaShOLVQG3g%
> 2BihzPCLme27n3c8ZaaMbaXR0A%3D&reserved=0>
>
> On Fri, Dec 15, 2017 at 6:45 AM, RAHUL SURESH <drrahulsuresh_at_gmail.com<
> mailto:drrahulsuresh_at_gmail.com>> wrote:
> Hi users
>
> How can I use the parameter.par file generated using ffTK for GROMACS?
>
> How can I convert them to required itp, top and gro file formats?
> Thank you
>
>
> --
> Regards,
> Rahul Suresh
> Research Scholar
> Bharathiar University
> Coimbatore
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU.
> outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%
> 7C01%7CJoshua.Vermaas%40nrel.gov%7Ca9b6e93a8bb14298485f08d543d548a5%
> 7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636489505697944503&sdata=
> Ygx3q0f1OrfS%2B944X2Nc%2B6rv%2FheJcdbtd9wd1p9TzXs%3D&reserved=0>
> https://github.com/giacomofiorin.
> safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.
> com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%
> 7Ca9b6e93a8bb14298485f08d543d548a5%7Ca0f29d7e28cd4f5484427885aee7
> c080%7C0%7C0%7C636489505697944503&sdata=yBJT2TnoybSuNcXcbkPXPEgkY7%
> 2FSFMpbfwJUjmdSxuU%3D&reserved=0>
>
> 

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*