Dear Justin, Many thanks for your quick reply! I really appreciate it.
* The code requires all [moleculetype] directives to be numbered from 1. This has no relationship to the actual global atom numbers in the coordinate file. What must be true is that the atoms in the topology and coordinate files appear in the same order. I would just to confirm that the following is correct. All the atomic indices referred to in the “bonds” “angles” “dihedrals” blocks are in fact the line number of the atoms. They are not related to the “atom index” . In other words, if there are 78 lines in the “atoms” block, the following would be an invalid entry in the “bonds” block even if one of my atoms has an index “95”. [bonds] 69 95 1 Thank you in advance! Ling Notice of Confidentiality: The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, re-transmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error please contact the sender immediately by return electronic transmission and then immediately delete this transmission including all attachments without copying, distributing or disclosing the same. -- 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.
