Dear Gromacs users, I've been trying to solvate Podophyllotoxin in ethanol. I used chimera and acpype to create PPT and I got the .itp and .pdb files. For ethanol I used http://virtualchemistry.org/molecules/64-17-5/index.php .top and GAFF liquid structure .pdb file. Since some atomtypes match between PTOX.itp and ETA.itp, I changed atomtypes in PTOX to uppercase and when I try Energy Minimization, I get:
WARNING 1 [file PTOX.itp, line 6]: Overriding atomtype OS WARNING 2 [file PTOX.itp, line 7]: Overriding atomtype CA WARNING 3 [file PTOX.itp, line 8]: Overriding atomtype C WARNING 4 [file PTOX.itp, line 9]: Overriding atomtype O WARNING 5 [file PTOX.itp, line 10]: Overriding atomtype OH WARNING 6 [file PTOX.itp, line 11]: Overriding atomtype H1 WARNING 7 [file PTOX.itp, line 12]: Overriding atomtype HA WARNING 8 [file PTOX.itp, line 13]: Overriding atomtype HC WARNING 9 [file PTOX.itp, line 14]: Overriding atomtype HO WARNING 10 [file PTOX.itp, line 15]: Overriding atomtype H2 Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: /home/john1990/code/gromacs-4.5.5/src/kernel/topio.c, line: 656 Fatal error: Syntax error - File ETA.itp, line 13 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This is the order in my topology file: ; Include forcefield parameters #include "amber99sb.ff/forcefield.itp" ;Include PTOX topology #include "PTOX.itp" ; Include ethanol topology #include "ETA.itp" Is there any way to fix it? Thanks in advance, Best regards, Hovakim Grabski Russian-Armenian(Slavonic) University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
