Re: [gmx-users] atomtype names case INsensitive?
Probably Mark On Jun 20, 2013 11:42 AM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atomtypes.atp are modified with all the atomtype names with lowercases thinking that it will avoid over riding and mixing of parameters (as some of angles and dihedrals are common). for example (there are many) WARNING 4 [file A.top, line 342]: Overriding Ryckaert-Bell. parameters. showing old and new values. The old values are from modified oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype names. Using gmxdump I can see system B is using modified oplsaa.ff. So does this mean Gromacs is case insensitive as I get warning even I used lowercase letters? regards, -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] atomtype names case INsensitive?
Hi, GROMACS is indeed case insensitive when it comes to atomtypes. I had the same problem a while ago. The simplest way to deal with it is just to add a letter at the end of your atomtypes. 2013/6/20 Mark Abraham mark.j.abra...@gmail.com Probably Mark On Jun 20, 2013 11:42 AM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atomtypes.atp are modified with all the atomtype names with lowercases thinking that it will avoid over riding and mixing of parameters (as some of angles and dihedrals are common). for example (there are many) WARNING 4 [file A.top, line 342]: Overriding Ryckaert-Bell. parameters. showing old and new values. The old values are from modified oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype names. Using gmxdump I can see system B is using modified oplsaa.ff. So does this mean Gromacs is case insensitive as I get warning even I used lowercase letters? regards, -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] atomtype names case INsensitive?
Thanks Mark and Baptiste, yes its case insensitive for atomtype names. I have changed all names and its working now :-) regards, On Thu, Jun 20, 2013 at 2:55 PM, Baptiste Demoulin bat.demou...@gmail.comwrote: Hi, GROMACS is indeed case insensitive when it comes to atomtypes. I had the same problem a while ago. The simplest way to deal with it is just to add a letter at the end of your atomtypes. 2013/6/20 Mark Abraham mark.j.abra...@gmail.com Probably Mark On Jun 20, 2013 11:42 AM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atomtypes.atp are modified with all the atomtype names with lowercases thinking that it will avoid over riding and mixing of parameters (as some of angles and dihedrals are common). for example (there are many) WARNING 4 [file A.top, line 342]: Overriding Ryckaert-Bell. parameters. showing old and new values. The old values are from modified oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype names. Using gmxdump I can see system B is using modified oplsaa.ff. So does this mean Gromacs is case insensitive as I get warning even I used lowercase letters? regards, -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
