[gmx-users] amber99sb_virtual site lipids dopc MCH3_N constraint types
Mark.Abraham at anu.edu.au
Tue Mar 27 18:20:36 CEST 2012
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?
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