[gmx-users] Regarding Trjconv.and ligand -protein complex simulation.......

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 2 07:11:43 CET 2010

On 02/02/10 16:50, PAVAN PAYGHAN wrote:
> Thnx for replying
> A]
> As i hv mentioned previously that in  my simulation  g_rms suggests it
> has some large peaks ,so applied trjconv with
> -pbc nojump now ...
>   there are no peaks in rmsd its oky but in vmd it showed that water is
> not having defined box so how to tackle this situation......
> 1.which -pbc option u suggests for this situation

Read trjconv -h, create a test case with only a few frames, and try out 
things that seem reasonable.

> 2.is <http://2.is> it possible to use two -pbc options together?

No, but it is normal to consider using several iterates trjconv if you 
want to massage things to look right to you.

> 3.is <http://3.is> it possible to modify the .xtc that i have generated
> with -nojump further to have defined box.

Probably, whatever you mean by that.

> B]
> my next question is with gromacs version 3.3.2
>   if im using NMR structure i need to give -ignh  option in pdb2gmx to
> ignore hydrogens or it will be taken care of  automatically.

Did you read pdb2gmx -h, and then try it and see? Experience is the best 

>   C]
>   Will u please give me any tutorial on ligand-dna/protein simulation
> either with PRODRG or ANTCHAMBER for drug input preparation.

Please start by searching the GROMACS webpage and Google first. You may 
discover alternatives to your preconceived solutions.


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