[gmx-users] Amino terminus atom types

[Lieven Buts]

I am trying a simple simulation of a protein in water using the OPSL-AA force 
field in Gromacs 3.1.4. The N terminus looks like this in the topology file:

----------------------------
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein_B           3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    
chargeB      massB
     1       MNH3      1    GLN    MN1      1          0    8.51535 
     2       MNH3      1    GLN    MN2      1          0    8.51535 
     3   opls_287      1    GLN      N      1       -0.3          0 
     4   opls_290      1    GLN     H1      1       0.33          0   
     5   opls_290      1    GLN     H2      1       0.33          0   
     6   opls_290      1    GLN     H3      1       0.33          0   
     7  opls_293B      1    GLN     CA      2       0.25     13.019   
...
----------------------------

Energy minimization works fine, but when I start a position-restrained run, I 
get these LINCS warnings:

----------------------------
Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000000 (between atoms 1 and 2) rms nan
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
----------------------------

at every step.

Is this a problem?



Cheers,

-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel