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 wrote: > 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 > > > Probably > > > > Mark > > On Jun 20, 2013 11:42 AM, "gromacs query" > 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
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 > Probably > > Mark > On Jun 20, 2013 11:42 AM, "gromacs query" 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?
Probably Mark On Jun 20, 2013 11:42 AM, "gromacs query" 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