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.
-Justin
best
karbalaee
--
========================================
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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