VMD-L Mailing List

From: Suresh Ghimire (suresh.ghimire2049sg_at_gmail.com)
Date: Sun Dec 17 2017 - 01:34:20 CST

Dear user
how can I use vmd mailing list?

On Sat, Dec 16, 2017 at 11:57 AM, RAHUL SURESH <drrahulsuresh_at_gmail.com>
wrote:

> 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%2Fpub
>> s.acs.org%2Fdoi%2Fabs%2F10.1021%2Facs.jcim.6b00103&data=
>> 02%7C01%7CJoshua.Vermaas%40nrel.gov%7Ca9b6e93a8bb14298485f08
>> d543d548a5%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C6364
>> 89505697944503&sdata=jTeg20SOaShOLVQG3g%2BihzPCLme27n3c8ZaaM
>> baXR0A%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
>> ok.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%
>> 7CJoshua.Vermaas%40nrel.gov%7Ca9b6e93a8bb14298485f08d543d548
>> a5%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636489505697
>> 944503&sdata=Ygx3q0f1OrfS%2B944X2Nc%2B6rv%2FheJcdbtd9wd1
>> p9TzXs%3D&reserved=0>
>> https://github.com/giacomofiorin.
>> protection.outlook.com/?url=https%3A%2F%2Fgithub.com%
>> 2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C
>> a9b6e93a8bb14298485f08d543d548a5%7Ca0f29d7e28cd4f5484427885a
>> ee7c080%7C0%7C0%7C636489505697944503&sdata=yBJT2TnoybSuNcXcb
>> kPXPEgkY7%2FSFMpbfwJUjmdSxuU%3D&reserved=0>
>>
>>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>