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

Song Ke song.ke at univie.ac.at
Tue Mar 27 14:54:35 CEST 2012

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?

Many thanks in advance,

Song KE
PhD Candidate
Mailto:song.ke at univie.ac.at
Molecular Modeling Lab
Department of Pharmacology and Toxicology
University of Vienna
Althanstrasse 14 (UZA 2)
A-1090 Vienna, Austria

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