[gmx-users] Regarding Trjconv.and ligand -protein complex simulation.......
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
> 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.
> 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
> 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.
More information about the gromacs.org_gmx-users