On 12/1/13 9:51 PM, rdwducl wrote:
Hello, I am trying to use implicit solvation but I am getting the following error from the preprocessor: ------------------------------------------------------- Program grompp_mpi, VERSION 4.6.4 Source code file: /home/robert/Research/Software/gromacs-4.6.4/src/kernel/topio.c, line: 734 Fatal error: Syntax error - File gbsa.itp, line 1 Last line read: '[ implicit_genborn_params ]' Invalid order for directive implicit_genborn_params For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- My topology file: #include "ffG45a3.itp" #include "cta.itp" #include "ions.itp" #include "gbsa.itp" [ system ] CTAC micelle implicit [ molecules ] CTA 80 CL- 80 The #includes are pretty self-explanatory but here is the head of gbsa.itp: [ implicit_genborn_params ] C16 1.0 1 1.0 0.207 1.0 C15 1.0 1 1.0 0.207 1.0 C14 1.0 1 1.0 0.207 1.0 ... I have read the manual regarding the order of directives in the topology file but that hasn't helped me. Perhaps I'm just tired. Can anyone see the problem?
All force field-level directives must be #included before any molecule-level directives (e.g. [moleculetype]) can be declared. Think of it this way: you have to define all of the parameters of all of the atom types before any of those types can be used within molecules. Therefore, gbsa.itp must be #included second in the list.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.
