[gmx-users] Need to Sort Out

[Johnny Lu]

Hi. I'm quite new to molecular dynamics too.

How did you make that itp? Does your system contain only one protein/DNA
molecule?

May be try this tutorial for a single protein?
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/

Check multiple journal papers when you decide how to simulate (even if you
are just simulating a single small protein).
Some systems might need different simulation steps. And, depending on the
things that you want to look at, you might have to stage a different
simulation.

On Sat, Dec 13, 2014 at 1:46 PM, Devender Arora <devarora at hotmail.com>
wrote:
>
> I am facing a problem in Gromacs while running grommp please do give the
> right direction I am new to Molecular dynamics.
>
>
> Fatal error:
> Syntax error - File topol_Protein_chain_A.itp, line 6966
> Last line read:
> '[ molecules ]'
> Invalid order for directive molecules
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> :
>
>
> Thanks & Regards
>
>
> Devender Arora
>
>
> Ph.D Scholar
>
>
> Department of Biotechnology
>
>
> GB Pant engineering College
>
>
> Pauri Garhwal, Uttarakhand
>
>
> Contact No. +919720045608, +91986896786
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>