Matthew L. Danielson wrote:
Ramachndran,
If you are trying to use the AMBER force field ports for Gromacs
(assuming you installed them correctly), I have defined the HEME group
for Amber03. If this would help you let me know, and i can provide the
files that you need to replace in your gromacs "top" folder
This sort of thing would make a nice addition to the "User Contributions" on the
Gromacs site, if you're willing to make them widely available to the public :)
-Justin
-Matt Danielson-
//
Justin A. Lemkul wrote:
Ramachandran G wrote:
Dear all,
It is known that force field for the heme group doesn't exist
in gromacs. So i tried to use amber force fields(AMBER94, AMBER99,
That's not true; all of the Gromos variants have heme parameters.
AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest
gromacs version 4.0.5 but still it gives the error message
'Residue 'HEME' not found in residue topology database'
Can anyone help me how to solve this problem. Thanks for your help.
Well, what is it that you tried? The error message is quite clear -
you do not have a [ HEME ] directive in the .rtp file for whatever
force field you're trying to use.
-Justin
Rama
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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