On 1/08/2012 11:29 PM, juanjuan0618 wrote: > Dear professor, > Now I want to simulate the water and carbon dioxide mixture solution,but > when I do the simulation with my own .gro and .itp files, I met some > questions. > I use gromacs4.0.7 and the water model is TIP4P2005. > Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars), > .top > and .mdp files, it prompts me > WARNING 1 [file co2.itp, line 3]: > Overriding atomtype C > WARNING 2 [file co2.itp, line 4]: > Overriding atomtype O > how can I remove these warning?
Define them with unique names if they should be distinct, or don't redefine them if they should be the same as the ones in the force field. > Q2: when I grompp the other .gro with a water cage(20 water moleculars) > containing a CO2 molecular and 1240 water moleculars, it prompts me > Syntax error - File co2.itp, line 1 > Last line read: > '[ atomtypes ]' > Invalid order for directive atomtypes > Can you tell me how I could remove this error? You've probably got some bizarre line ending or non-text formatting. Plain text, preferably with unix-style line endings, will work. dos2unix tool may be your friend. Thank you very much for your answers, Question 1 has been solved, but the second question is still appearing. I try to change the file style to unix by using dos2unix, but the problem isn't solved. When I change the order of the including file of the topology file, it may prompts me Syntax error - File tip4p.itp, line 4 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype or prommpt me Syntax error - File co2.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I can't find what's error, and I don't know how to solve the problem. Can you tell me what could I to remove this error? http://gromacs.5086.n6.nabble.com/file/n4999956/co2.itp co2.itp http://gromacs.5086.n6.nabble.com/file/n4999956/co2-01-00.top co2-01-00.top Looking forward to your reply, thank you very much. -- View this message in context: http://gromacs.5086.n6.nabble.com/atomtypes-are-not-case-sensitive-tp4426581p4999956.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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