[gmx-users] A problem of adding new bond parameters

[spin]

Hello, everyone,
    I have tried to create a mutant of CYS, the CYC, which the S was
replaced with a C at the end of its side chain. After using pdb2gmx to build
the .top file, I added bond and nonbond parameters to link the side chain of
two CYC as the disulfide bond for CYS. Also all necessary force field
parameters have been added, especially those in ffbonded.itp and
ffnonbond.itp. But when I use grompp, it give the following information:
  /ERROR 1 [file TP-2.top, line 421]:
  No default Bond types/
  There are 45 errors like this. The atom types of the side chain of CYC are
described by GCenFF and those of the main chain are described by CHARMM.
There are bond types, angle types and dihedral types of atoms from both the
main side and the side chain. I created them just by replace the CHARMM atom
types with GCenFF atom types of the side chain. For example, the angle type
*HB   CT2   CT1* was replaced with *HGA2	 CG321	 CT1*. 
  Later I found that there were angle types and dihedral types in .top file
missed in ffbonded.itp for both CYS and CYC. The topology of CYS can be
recognized normally by grompp, while the one of CYC can not. Can someone
tell me the reason?

Thank you!

Qing Liu



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