[gmx-users] Problem when adding new residue in itp file

[Justin A. Lemkul]

Du Jiangfeng (BIOCH) wrote:
> Hi Guys,
> 
> I want to run a protein which contains some carboxylated residues into a membrane. I have had to add a special residue into itp file since there is no any description in normal itp for GLA residue. I admit some values I added for GLA residue were ambiguous because I don't know the exact values.
> 
> After that, the system was blowing up when MD simulation with the following warning:
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.029057, max 0.152326 (between atoms 81 and 82)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      43     44   37.0    0.0145   0.0148      0.0145
>      81     82   67.5    0.0078   0.0090      0.0078
>      89     90   34.7    0.0059   0.0060      0.0059
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.056864, max 0.359219 (between atoms 81 and 82)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      43     44   35.6    0.0145   0.0147      0.0145
>      81     82   78.6    0.0078   0.0106      0.0078
>      89     90   34.3    0.0059   0.0060      0.0059
> 
> 
> Apparently, some values about GLA residue are wrong in itp file. But I really don't know how to set a correct value for it.
> 

Without seeing what you actually did and knowing what force field you're using, 
it's impossible to help.  Missing parameters need to be derived in a manner 
compatible with the original force field (no small task).

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

-- 
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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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