[gmx-users] Editing of the existing system

James Starlight jmsstarlight at gmail.com
Sat Mar 31 13:31:20 CEST 2012


I've forced with some problems during MDrun of such system with the two

Firstly, after addition of second protein, I've removed all water and ions
and solvated my system with genbox and genion.

Than I've redefined groups of my proteins ( wich are like a_1-4000 and
a_4001-5000 ) in index.ndx file in the separate T_coupl, COM and
energygroups because atom order was perturbed after solvation.

Than I've minimized my system  with the Emtool=500

The problems were on the nvt equilibration phase with the posres applied on
the both proteins. I have no errors, notes or warninngs from GROMPP but
when I've started my simulation with MDrun my system was crushed on the 1st
step with the multiple LINKS warnings as well as message that something
wrong with interactions between 1st protein atoms and surrounded water ( as
I've said previously after addition of the second protein to my system I've
resolvated my system again).

Might my system be not properly minimized  or does something wrong else in


31 марта 2012 г. 2:20 пользователь Mark Abraham
<Mark.Abraham at anu.edu.au>написал:

>  On 31/03/2012 1:00 AM, James Starlight wrote:
> Mark,
> Also I'd like to know some more about most correct parametrisation of such
> new edited system. My new system consist of two proteins ( one- wich was
> initially and the second small peptide wich I've docked to the first
> protein). So now I need to define 2 separate groups for the below enties of
> my MD files
> energygrps = Protein peptide
> tc-grps     = Protein_Bilayer SOL_ions_peptide
> and finally CoM groups because of the general anisotropy of the membrane system
> comm-grps	= Protein_Bilayer SOL_Ions_Peptide
> I've made itp file for the peptide via pdb2gmx so in th default definition both the protein and peptide are the protein enty in the index file.
> I've separate both of the protein and peptide by selection of two subsets of atoms wich represent to the each of that enties.
> So finally I have two groups in the index.ndx file
> a_1-5000  ( it's protein)
> a_9999-10500 (it's peptide)
> You can use make_ndx (or a text editor on the .ndx file) to give them more
> helpful names.
>  Does this separation correct in general ? I have some fears because both protein and peptide consist of the same residue numbers in the GRO file ( e.g there are 212- lys wich is part of the protein and 212-Pro wich is part of the peptide ) Might this system be tended to errors?
> Residue numbers are largely irrelevant. pdb2gmx and maybe grompp use them
> for matching a coordinate file to the .rtp and .top (respectively), but
> only really in the sense that the number changes from one residue to
> another.
>  I have no errors during processing of that sustem by grompp as well as md run. What should I do for such system consisted of two proteins in separate phases ( membrane-like and water)
> ?
> All seems basically sound.
> Mark
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120331/e74fabaf/attachment.html>

More information about the gromacs.org_gmx-users mailing list