Hi Kenji, I guess if you change/swap the order of molecules in top file it will work. The order of molecules in your gro file should match up with your top file. If you give us more info it would be good :) I am just guessing :(
[ molecules ] SOL 1088 LJN 1 Swap them like this Cheers, EB -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Kenji Mochizuki Sent: Monday, 28 January 2013 3:46 PM To: [email protected] Subject: [gmx-users] making .top file of new LJ in Water Dear gmx users I would like to start MD simulation for GAS Hydrate, consisting of TIP4P and LJ representing N2. I have made .top file by hand as following. When I use grompp_d for making .tpr file, I got the following error. However, LJ name in .gro file is same as in .top file, which is "NX" I am not sure what is wrong. Could you please give me some advise ? Regards === error === WARNING 1 [file GAS_Hydrate.top, line 25]: 4353 non-matching atom names atom names from GAS_Hydrate.top will be used atom names from N1088-N2.gro will be ignored === .top file ==== #include "ffoplsaa.itp" ;----Nitrogen Molecule--------- [ atomtypes ] NX NX 0.0000 0.0000 A 3.69800e-01 0.787014e+00 [ moleculetype ] LJN 3 [ atoms ] 1 NX 1 LJN NX 1 0.00000 28.000000 ;--- TIP4P -- #include "tip4p.itp" [ system ] GAS Hydrate [ molecules ] LJN 1 SOL 1088 ==============================- Kenji Mochizuki -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
