The warning is due to having the molecules in the topology .top file listed in a different order to how they appear in the coordinate file, .gro
The list within the topology has to be in the same order, even if you have broken up groups of the same molecules in the coordinate file. As for the error. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of trevor brown Sent: Thursday, 20 January 2011 10:51 AM To: gmx-users@gromacs.org Subject: [gmx-users] CNT Hi Justin, I added lines to ffnonbonded.itp. It resulted in following error. It has some warnings and an error. I am interested in error. After that I will look at the warnings. In which file we may have an error? It is not specified. best wishes trevor Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations Excluding 5 bonded neighbours molecule type 'ICE' Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Warning: atom name 170 in topol.top and final2.gro does not match (H1 - CA) Warning: atom name 171 in topol.top and final2.gro does not match (H2 - C) Warning: atom name 172 in topol.top and final2.gro does not match (H3 - O) Warning: atom name 173 in topol.top and final2.gro does not match (CA - CB) Warning: atom name 174 in topol.top and final2.gro does not match (HA - CG) Warning: atom name 175 in topol.top and final2.gro does not match (CB - CD1) Warning: atom name 176 in topol.top and final2.gro does not match (HB1 - CD2) Warning: atom name 177 in topol.top and final2.gro does not match (HB2 - HA) Warning: atom name 178 in topol.top and final2.gro does not match (CG - HB1) Warning: atom name 179 in topol.top and final2.gro does not match (HG - HB2) Warning: atom name 180 in topol.top and final2.gro does not match (CD1 - HG) Warning: atom name 184 in topol.top and final2.gro does not match (CD2 - HD21) Warning: atom name 185 in topol.top and final2.gro does not match (HD21 - HD22) Warning: atom name 186 in topol.top and final2.gro does not match (HD22 - HD23) Warning: atom name 187 in topol.top and final2.gro does not match (HD23 - H1) Warning: atom name 188 in topol.top and final2.gro does not match (C - H2) Warning: atom name 189 in topol.top and final2.gro does not match (O - N) Warning: atom name 190 in topol.top and final2.gro does not match (N - CA) Warning: atom name 191 in topol.top and final2.gro does not match (H - C) Warning: atom name 192 in topol.top and final2.gro does not match (CA - O) (more than 20 non-matching atom names) WARNING 2 [file topol.top, line 39]: 184 non-matching atom names atom names from topol.top will be used atom names from final2.gro will be ignored There were 2 warnings ------------------------------------------------------- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s)
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