[gmx-users] generation of tfe solvent box

[Tsjerk Wassenaar]

Prasun,

You're really messing things up here! You should get to terms with the
gromacs manual. Read up on the different file types and how things are
connected. To start with, gromacs doesn't care whether it's given a
.pdb file or a .gro file for coordinates. So everywhere where it says
you can read/write a .gro file, you can read/write a .pdb file (vv).

Whatever you're doing (from what you mention) has nothing to do with
an .rtp file. Where did you come up with that? The .rtp files are
building block libraries for constructing topologies for (bio)polymers
and are _only_ used by pdb2gmx (to generate a .top/.itp topology
file). What you have to do is to take your single TFE [ moleculetype ]
description and use it to build a topology for your [ system ]
consisting of 1000 TFE molecules. Check out the corresponding files in
the gromacs tutorial for simulating a water box. And do read chapter 5
of the manual (and preferrably the preceding ones too).

Cheers,

Tsjerk

On Thu, Jul 10, 2008 at 9:20 AM, prasun kumar <prasun30 at gmail.com> wrote:
> hello,
> i would like to generate a TFE solvent box for my simulation.I have created
> a pdb file containing the 1000 TFE molecules in the cubic cell having
> dimension 40.Now i want to convert it into gro file and call it in the
> gromacs simulation .
> can any one help me in generating gro file of TFE.I have "tfe.itp" file.
> Should I change something in the *.rtp file.
> I tried using PRODRG but it has limitations of only 300 atoms.
> I am gettin error like this
> PRODRG cant model most non carbon -halogen bonds
> can any one help me in getting gro file for TFE.
> Thanx in advance
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623