[gmx-users] specbonds are not taken by gromos force field?

[Justin Lemkul]

On 4/19/13 10:45 AM, 라지브간디 wrote:
> Hello gromacs.
>
>
> I wanna simulate the heme contain proteins which has bond FE-NE2 from HIS as it already found in specbond section.
>
>
> When i use pdb2gmx, I could see the links of these but in topology file but not parameter information which detects from ffbonded.itp.
>
>
> I also checked the ffbonded.itp file and found that it has default parameter information for heme links with his, which also described in specbond column.
>
>
> What can be done to pdb2gmx to detect these bond parameter from ffbonded.itp file?
>
>

Can you please provide an exact example of what the issue is?  Your question 
conflicts itself - first you say the parameters are not looked up in 
ffbonded.itp, but then you say the parameters are there.  There are frequent 
reports of issues with heme in Gromos96 force fields, but none ever seem to get 
resolved, usually due to lack of information.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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