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

[Justin A. Lemkul]

prasun kumar 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 <http://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

I think Tsjerk has already given you a nice, detailed explanation.  The problem 
is you have not done the leg work of reading the relevant manual sections.

In general, as I say several times a day it seems, when asking for free help, 
make it easy: show exact error messages (copied and pasted from the screen 
output) so we know exactly what's going on.

Basically, you will need to define parameters for the TFE molecule in an .itp 
file (I suspect your previous message was in relation to this fact?). 
Furthermore, parameters for TFE already exist in $GMXLIB/top.  If you do not 
want to use these, use this tfe.itp file as the template for what you create.

Tutorial material (some of which Tsjerk already recommended to you) and the 
manual/wiki will provide you with the answers you need.

-Justin

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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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