vivek sharma wrote:
Hi All,
I am trying to run the tutorial
"http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs"; for using
ACPYPI generated topology with GROMACS.
I am using amber99sb forcefield for one docked complex. It is running
successfully upto genion and giving error while doing grompp for energy
minimization
----------
-------------------------------------------------------
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1641
Fatal error:
No such moleculetype Na
-------------------------------------------------------
I tried adding ions entries from amber99sb.rtp to ions.itp and ended up
with same error.
I tried instruction given at
"http://www.mail-archive.com/[email protected]/msg20965.html"; which
also resulted in same error.
I was able to successfully perform EM as well as MD without adding ions
i.e bypassing the genion step.
Please, suggest me the way to get rid of this error.
Can you post the relevant entry in ions.itp? If you followed the instructions
at the link you posted correctly, then you shouldn't have this problem. Maybe
someone can spot the mistake.
-Justin
With thanks,
Vivek
--
========================================
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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