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

[Du Jiangfeng (BIOCH)]

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.

Anybody can help me? Thanks millions,

Jiang.