Dear Peter,
Thank you, I find the answer now. Sorry I was using a pdb that the SS length is too long to form the SS bond. After changing to a correct one, I got the solution. I think, if we have more than one chain, we MUST use "-merge" option, so that the interchain SS bond can shown in the generated itp file. If "-merge" is missing, only the intra-chain SS bonds are shown in the individual itp files. So happy to see the martini forum come back! Yours sincerely Cheng ------------------ Original ------------------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 29, 2019 11:03 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: How to set the inter-chain disulfind bond in martini? Dear Martini friends, My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy chain (HC): ) Interchain disulfide bond: LC214 ?C HC220 ) Intrachain disulfide of LC: LC23 ?C LC88, LC134 ?C LC194 ) Intrachain disulfide of HC: HC144 ?C HC200, HC96 ?C HC22 Using this command will only generate four intrachain disulfide bonds, without the interchain one: $ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp ./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H prompt: $ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying closer than 0.2200 nm $ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG', 'CYS', 88, 'L') (0.204094 nm) $ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG', 'CYS', 194, 'L') (0.204489 nm) $ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG', 'CYS', 434, 'H') (0.203603 nm) $ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG', 'CYS', 414, 'H') (0.204830 nm) I can see the four disulfide bonds information is reflected in the [ constraints ] section of "Protein_L+Protein_H.itp" file: $ 45 191 1 0.24000 ; Cys-bonds/special link $ 294 431 1 0.24000 ; Cys-bonds/special link $ 475 947 1 0.24000 ; Cys-bonds/special link $ 778 900 1 0.24000 ; Cys-bonds/special link So how to also ensure the intactness of the interchain disulfide bond? You can find my files at https://github.com/lanselibai/martini/tree/master/20190129_disulfide Thank you! Yours sincerely Cheng -- 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.