[gmx-users] Atomtype:CB

[pkmukher]

Hello users,

  I found a problem similar to one described in the mailing
list. The problem occurs in grompp wherein it says
unrecognized atom type CB. As suggested in the mailing list
the problem arises when in a ligand protein system the
ligand is prepared using the PRODRG server GROMOS87 format
and the protein is prepared in some other FF..in my case
43a1(GROMOS96)..when i prepared my protein using the -ff gmx
flag (gmx Gromacs Forcefield (a modified GROMOS87)) grompp
did not have any problems. My question is that is there a
way to prepare the ligand in 43a1 format so that when i run
grompp the relevant input files are is the same desired
format. Thanks in advance 

Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell   - 662 380 0146
Office - 662 915 1286