[gmx-users] tfe

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 14 12:01:16 CEST 2008

shahrbanoo karbalaee wrote:
> Dear mark and justin
> hi,thank you for your advices.
> I want to make simulation peptide in 30%tfe.I get tfe.pdb and take
> tfe.gro from prodrug program.I make solvatedtfe.gro and the other
> solvatedspc.gro.then I make 30mol tfe and 70 spc in a file by
> hands.and then run genbox -f .....cs 3tfe70spc.gro ....this command
> run and it give me solvated peptide in 30tfe and 29spc.I surprised for
> number solvent (I expected near 1500to 3000 because peptide has 13 aa
> and box -d 0.7)any way  I run grompp after edit topology file (the
> number solvents  and add  include tfe.itp).but it give error and this
> is answe:I dont find typeC and error in toputil .I check my topology
> file  but I dont find error.please help me?

Please copy and paste the exact error message, but I suspect you have included 
the TFE topology incorrectly, either by making a typo or by including it in the 
wrong order.  Check your .top carefully.

I would back up and examine why you only have 29 water molecules in your system. 
  I guarantee something has gone wrong.  One should not plow ahead when strange 
behavior appears.


> best
> karbalaee


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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