[gmx-users] specbond .dat fie : any one plz modify it......tell me how to modify it..
mehreen_jan1990 at yahoo.com
Wed Feb 8 08:47:54 CET 2017
Hello, anyone plz help
Hopefully you all are doing well.
I am using FF: 43a1
I know parameters for Heme are already available and that is for FE2+. I want to perform MD simulation for FE3+. While running simulation I get error : Residue "OXY" not found in residue topology database. I checked .rtp file and that does not include topology for OXY. I checked gromacs mailing list and got the answer that modify specbond . dat file . Kindly please brief me how should I modify specbond .dat file so that I could include oxygen molecule. i read manual 5.6.7 Special bonds but i am still not able to connect OXY with HEME. This is my oxygen
HETATM 2414 O1 OXY C1543 5.525 80.353 -6.212 1.00 25.38 O
HETATM 2415 O2 OXY C1543 4.301 80.342 -6.721 1.00 30.35 O
specbond .dat fie : any one plz modify it......
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 1 HEM FE 2 0.25 CYS2 HEME
CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
MET SD 1 HEM FE 1 0.24 MET HEME
CO C 1 HEME FE 1 0.19 CO HEME
CYM SG 1 CYM SG 1 0.2 CYS2 CYS2
CYZ SG 1 ZN1 ZN 1 0.23 CYZ ZN1
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