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
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