Hello, Sorry, I realised the HEME HEC naming was not the problem. But still the pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets protonated and doesnot form a bond with HEME. I tried to preserve the bonds by editing the specbond.dat file. I do not know if it can be used for intramolecular bonding. Kindly inform if the modifications I have made are valid. The runtime information during the execution of pdb2gmx indicated the linking of FE in HEME to the N atoms. However, I do not see the bonds when I open the output file in Pymol. Please indicate how this problem can be resolved.
This is the content of my specbond.dat file: 5 CYS SG 1 HEME FE 5 0.25 CYS HEME HEME FE 5 HEME NA 3 0.22 HEME HEME HEME FE 5 HEME NB 3 0.22 HEME HEME HEME FE 5 HEME NC 3 0.22 HEME HEME HEME FE 5 HEME ND 3 0.22 HEME HEME And these I obtained during the execution of pdbgmx: Opening library file specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Special Atom Distance matrix: CYS122 CYS135 CYS143 CYS146 CYS150 CYS237 CYS309 SG958 SG1059 SG1118 SG1136 SG1165 SG1902 SG2475 CYS135 SG1059 1.677 CYS143 SG1118 1.076 1.092 CYS146 SG1136 1.313 1.792 0.749 CYS150 SG1165 1.175 2.054 0.978 0.426 CYS237 SG1902 2.194 3.510 2.536 1.933 1.632 CYS309 SG2475 1.745 2.703 2.469 2.507 2.423 2.449 CYS343 SG2748 4.679 4.998 4.364 3.763 3.870 3.329 4.426 CYS406 SG3265 2.258 2.657 2.051 1.603 1.744 1.886 2.198 CYS457 SG3657 2.232 0.829 1.894 2.582 2.825 4.173 2.898 HEME462 FE3693 2.257 2.566 1.949 1.489 1.669 1.956 2.343 HEME462 NA3694 2.456 2.680 2.110 1.663 1.862 2.118 2.486 HEME462 NB3695 2.199 2.426 1.883 1.498 1.704 2.088 2.247 HEME462 NC3696 2.061 2.462 1.795 1.321 1.479 1.809 2.217 HEME462 ND3697 2.331 2.711 2.031 1.505 1.657 1.841 2.455 CYS343 CYS406 CYS457 HEME462 HEME462 HEME462 HEME462 SG2748 SG3265 SG3657 FE3693 NA3694 NB3695 NC3696 CYS406 SG3265 2.501 CYS457 SG3657 5.547 3.210 HEME462 FE3693 2.512 0.219 3.147 HEME462 NA3694 2.361 0.325 3.240 0.211 HEME462 NB3695 2.647 0.293 2.977 0.208 0.295 HEME462 NC3696 2.671 0.286 3.064 0.209 0.420 0.297 HEME462 ND3697 2.389 0.314 3.318 0.208 0.297 0.416 0.293 Linking HEME-462 FE-3693 and HEME-462 NA-3694... Linking HEME-462 FE-3693 and HEME-462 NB-3695... Linking HEME-462 FE-3693 and HEME-462 NC-3696... Linking HEME-462 FE-3693 and HEME-462 ND-3697... N-terminus: PRO-NH2+ C-terminus: COO- Now there are 462 residues with 4749 atoms Making bonds... Thanks. Sarada Graduate Student, NCBS, Bangalore Hello, I am working with the simulation of cytochromeP450. In the output of the pdb2gmx command, the iron atom in the HEME loses all the bonds, including the sulphide bond with cystine. Also, the command changed the residue name from HEME to HEC. During the execution of the pdb2gmx, I get this warning: Warning: 'HEC' not found in residue topology database, trying to use 'HEME' Can someone please tell me, if this is responsible for the loss of bonds especially the one between CYS and FE. How can the bonds be retained? Thanks. Sarada _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php