[gmx-users] tfe.gro file and generation of .itp file

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Jul 13 10:26:29 CEST 2008


Starting with the end (the last question is easiest).

> Apart from this i am interested in learning how to create .itp
> file,can you please suggest any method.

Reading! A very good method of learning things. It's how I learned to
do these things.

> So can you please send me the detail procedure
> please.

NO! What do you expect, that I take my time to write you a 'detailed
procedure'? That's your homework! I'll give you pointers if you go
astray and if I feel I can help you solve your problem (and if I feel
up to giving free advice).

Then, you complain that you don't get what I say. That's because you
don't understand yet what there is to Gromacs (and maybe to MD). You
have to first take the trodden paths. In your case that means doing
water simulations as provided in the Gromacs distribution and get to
terms with the way gromacs deals with structure and topology files.
Then you can go to the next stage, and that would be a single molecule
of TFE (in water).

In the mail I replied to you stated "I already have itp file". So,
that's what I assumed you did. We only know as much as you provide for
information. And if you say you have an .itp file, but you don't, it's
your problem if you don't understand my reply (although it seems to be
a waste of my time). This makes clear that you have to choose your
wording carefully when posting a question on a (any) user list.

It seems to me you want too much in too little time. It will take an
effort getting to terms with Gromacs. That's an investment ;)



On Sat, Jul 12, 2008 at 7:53 AM, prasun kumar <prasun30 at gmail.com> wrote:
> Dear Tsjerk A
> I am not getting you what you have told.I tried to do it by another way
> also.first generate the box of dimension 3 with 10 molecules of TFE and then
> create the gro file one by one for every 10 molecules put it in the one file
> and saved it as tfe.gro.it works well till genbox,but after that for grompp
> its not workin givin error like TFE is not a defined molecule or cannot find
> force field for F molecule.So can you please send me the detail procedure
> please.Apart from this i am interested in learning how to create .itp
> file,can you please suggest any method.
> waiting for your reply
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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

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