From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Dec 18 2017 - 11:34:17 CST

1. Sure, it doesn't look the same, since it contains both the parameter set as well as the definition of the topology of the system. The parameter set is usually hidden in the files that are #included from the .top file. It'll work just fine for simulation.

2. VMD can write .gro files. Load your system into VMD, and "save coordinates". It defaults to pdb, but gro is also an option.

3. Anything you need an itp file for, you can do explicitly in the .top file! That is the beauty of the itp preprocessing gromacs does. The syntax is sometimes just a pain.

-Josh

On 12/15/2017 11:12 PM, RAHUL SURESH 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<mailto: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.html08d5444bfe79%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636490015546428794&sdata=9RyOPIlbnhfd%2FNT2C7fIvUXL2nEa6EUmvurLE8JPBIE%3D&reserved=0>). 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.6b00103f5484427885aee7c080%7C0%7C0%7C636490015546428794&sdata=7Pmoir5g%2B68Q4nUP%2Bg7nlstsz%2B2dJ71gZfUFfOhEfZI%3D&reserved=0><https://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%7Ca9b6e93a8bb14298485f08d543d548a5%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><mailto: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/Q3TBQUgAqaBdGEYjKtzGq1U%2BPmGwL%2Bo774%3D&reserved=0><https://na01.safelinks.protection.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/giacomofiorin4&sdata=FMnEVUJfgQxhYMX5spbpHt8lSW7FzgtYVVxq9F9mF9w%3D&reserved=0><https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Ca9b6e93a8bb14298485f08d543d548a5%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636489505697944503&sdata=yBJT2TnoybSuNcXcbkPXPEgkY7%2FSFMpbfwJUjmdSxuU%3D&reserved=0>
--
Regards,
Rahul Suresh
Research Scholar
Bharathiar University
Coimbatore