[gmx-users] amber99sb_virtual site lipids dopc MCH3_N constraint types

[Mark Abraham]

On 27/03/2012 11:54 PM, Song Ke wrote:
> Dear All,
>
> I have a question about create and simulate dopc lipid virtual sites. I
> noticed in ffbonded.itp
>
> [ constrainttypes ]
> ; this section is implemented manually from bond&  angle values
>
> ; constraints for rigid CH3 groups
>   MCH3   CT      2    0.166426
>   MCH3   S       2    0.193875
>   MCH3   MCH3    2    0.092163
> ; constraints for rigid NH3 groups
>   MNH3   CT      2    0.158254
>   MNH3   MNH3    2    0.080229
>
> ; angle-derived constraints for OH and SH groups in proteins
> ; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C.
>    C     HO      2    0.195074
>    CA    HO      2    0.195074
>    CT    HO      2    0.194132
>    CT    HS      2    0.235935
>
>
> However, there is no MCH3 N constraint types, how can I get this value?
>
> Meanwhile, Is there a website or scripts to generate the dopc virtual
> sites bonded itp instead of do it manually?

What's unsatisfactory about pdb2gmx -vsite?

Mark