Hello, I'm running grompp on two small molecules in a single .gro file using the following topology file:
#include "ffgmx.itp" #include "BDEX.ITP" #include "AHL.ITP" #include "spc.itp" [ system ] BDEX AHL [ molecules ] BDEX 1 AHL 1 Part of my output looks like the following: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for BDEX 1 Excluding 3 bonded neighbours for AHL 1 processing coordinates... WARNING 1 [file "topol.top", line 12]: Bad box in file Complex.GRO Generated a cubic box 20.000 x 1.445 x 1.830 Warning: atom names in topol.top and Complex.GRO don't match (O2 - CAS) Warning: atom names in topol.top and Complex.GRO don't match (HAA - CAR) Warning: atom names in topol.top and Complex.GRO don't match (C2 - CAQ) Warning: atom names in topol.top and Complex.GRO don't match (C3 - CAP) Warning: atom names in topol.top and Complex.GRO don't match (O3 - CAO) Warning: atom names in topol.top and Complex.GRO don't match (HAB - CAN) Warning: atom names in topol.top and Complex.GRO don't match (C4 - CAM) Warning: atom names in topol.top and Complex.GRO don't match (O4 - CAL) Warning: atom names in topol.top and Complex.GRO don't match (C5 - CAK) Warning: atom names in topol.top and Complex.GRO don't match (C6 - CAJ) Warning: atom names in topol.top and Complex.GRO don't match (O6 - OAT) Warning: atom names in topol.top and Complex.GRO don't match (HAC - CAI) Warning: atom names in topol.top and Complex.GRO don't match (O5 - CAH) Warning: atom names in topol.top and Complex.GRO don't match (C1 - OAU) Warning: atom names in topol.top and Complex.GRO don't match (O1 - N) Warning: atom names in topol.top and Complex.GRO don't match (CAJ - HAA) Warning: atom names in topol.top and Complex.GRO don't match (CAK - CA) Warning: atom names in topol.top and Complex.GRO don't match (OBY - CB) Warning: atom names in topol.top and Complex.GRO don't match (CAL - CAA) Warning: atom names in topol.top and Complex.GRO don't match (OBZ - OAC) (more than 20 non-matching atom names) WARNING 2 [file "topol.top", line 12]: 120 non-matching atom names atom names from topol.top will be used atom names from Complex.GRO will be ignored - Complex.GRO consists of two molecules AHL and BDEX. -The ffgmx force field has already worked successfully with the BDEX.itp and molecule, but for some reason all but 2 of the AHL molecule atoms have the mismatch problem. Which file do I have to modify to clear the atom name mismatch issue? The atom names in question are identical between the Complex.gro and AHL.itp files, so I'm a bit confused. Any guidance you could provide would be appreciated. Regards, Marc _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
