[gmx-users] Amino terminus atom types

[David van der Spoel]

On Thu, 2003-11-20 at 13:55, Lieven Buts wrote:
> 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?
yes,

I'm working on it.

> 
> 
> 
> Cheers,
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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