sarah k wrote:
dear Justin,
I should appreciate your guides in this period. They're really helpful
but again, I have some problem:
I started over, several times as you suggested. I replaced the name of
SOL with N2. The problem of coordinates was solved by manual addition of
#N2 molecules to topol.top each time. But this error appears:
Program grompp_d,
Source file: topio.c, line: 587
Molecule type 'N2' contains no atoms
Be sure your naming is consistent - the [moleculetype] and whatever residue(s)
that are part of it are separate concepts.
I checked the program of topio, grompp, and etc but I couldn't find SOL
molecule type to know how I can fix it. Would you please give me an
idea? Is gromacs able to simulate in non-aqous condition?
Absolutely.
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
-Justin
Cheers,
Sarah K.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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