Hello everyone,
I have a problem related with a molecule with inter- and intra-chain disulfide bridges. When I convert my pdb file into a gromacs file, all the disulfide bridges are still connected (inter- and intra-chain). However, when I perform a short optimization of the structure (in vacuum), the inter-chain disulfide bridges are broken because the bond distance is too large (around 5 and 6 Å). My idea is to use distance restraint to limit the maximum distance between the different sulfure atoms to roughly 2 Å. However, my problem is that I do not know what residue names I have to use to differentiate the sulfuret atoms from different chains. Below, you can find two cysteines (from the itp file) from different chains that I would like to bind. The question is: If I want to use distance restraint between these two residues, what is the information that I have to put in the ai and aj fields of the position restraint table? Thank you very much for your help and happy new year for all of you. Oscar CYS in chain A ; residue 897 CYS rtp CYS2 q 0.0 315 NH1 897 CYS N 315 -0.47 14.007 ; qtot 2.53 316 H 897 CYS HN 316 0.31 1.008 ; qtot 2.84 317 CT1 897 CYS CA 317 0.07 12.011 ; qtot 2.91 318 HB 897 CYS HA 318 0.09 1.008 ; qtot 3 319 CT2 897 CYS CB 319 -0.1 12.011 ; qtot 2.9 320 HA 897 CYS HB1 320 0.09 1.008 ; qtot 2.99 321 HA 897 CYS HB2 321 0.09 1.008 ; qtot 3.08 322 SM 897 CYS SG 322 -0.08 32.06 ; qtot 3 323 C 897 CYS C 323 0.51 12.011 ; qtot 3.51 324 O 897 CYS O 324 -0.51 15.999 ; qtot 3 CYS in chain B ; residue 445 CYS rtp CYS q 0.0 3451 NH1 445 CYS N 3451 -0.47 14.007 ; qtot 5.53 3452 H 445 CYS HN 3452 0.31 1.008 ; qtot 5.84 3453 CT1 445 CYS CA 3453 0.07 12.011 ; qtot 5.91 3454 HB 445 CYS HA 3454 0.09 1.008 ; qtot 6 3455 CT2 445 CYS CB 3455 -0.11 12.011 ; qtot 5.89 3456 HA 445 CYS HB1 3456 0.09 1.008 ; qtot 5.98 3457 HA 445 CYS HB2 3457 0.09 1.008 ; qtot 6.07 3458 S 445 CYS SG 3458 -0.23 32.06 ; qtot 5.84 3459 HS 445 CYS HG1 3459 0.16 1.008 ; qtot 6 3460 C 445 CYS C 3460 0.51 12.011 ; qtot 6.51 3461 O 445 CYS O 3461 -0.51 15.999 ; qtot 6 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.