Re: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa
Thanks Berk, it seems to be working now. Alan On 24 August 2010 08:54, Berk Hess wrote: > Hi, > > This was due to two simultaneous issues. I fixed them both for the next > beta release. > Note that using HIS iso HISE as a residue name would solve the problem. > For 4.5 this should be the normal input, since residue names from the pdb > are now preserved. > > Berk > > -- > From: alanwil...@gmail.com > Date: Mon, 23 Aug 2010 17:45:03 +0100 > > To: gmx-users@gromacs.org > Subject: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa > > > Hi there, > > I have a system with 'HISE' and using gmx 4.5. > > ATOM 20 N HISE2 6.376 3.718 -0.053 1.00 0.00 > N > ATOM 21 H HISE2 5.980 4.646 -0.135 1.00 0.00 > H > ATOM 22 CA HISE2 7.843 3.744 -0.109 1.00 0.00 > C > ATOM 23 HA HISE2 8.260 3.319 0.806 1.00 0.00 > H > ATOM 24 CB HISE2 8.319 2.925 -1.327 1.00 0.00 > C > ATOM 25 HB2 HISE2 7.855 1.940 -1.312 1.00 0.00 > H > ATOM 26 HB1 HISE2 7.985 3.435 -2.233 1.00 0.00 > H > ATOM 27 CG HISE2 9.807 2.703 -1.450 1.00 0.00 > C > ATOM 28 ND1 HISE2 10.461 2.463 -2.655 1.00 0.00 > N > ATOM 29 CE1 HISE2 11.770 2.542 -2.382 1.00 0.00 > C > ATOM 30 HE1 HISE2 12.557 2.484 -3.124 1.00 0.00 > H > ATOM 31 NE2 HISE2 11.969 2.794 -1.078 1.00 0.00 > N > ATOM 32 HE2 HISE2 12.817 3.173 -0.672 1.00 0.00 > H > ATOM 33 CD2 HISE2 10.740 2.839 -0.459 1.00 0.00 > C > ATOM 34 HD2 HISE2 10.579 3.098 0.574 1.00 0.00 > H > ATOM 35 C HISE2 8.279 5.228 -0.214 1.00 0.00 > C > ATOM 36 O HISE2 7.440 6.079 -0.525 1.00 0.00 > O > > when trying: > > pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none > > Identified residue HISE1 as a starting terminus. > Identified residue HISE3 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Special Atom Distance matrix: >HISE1 HISE2 >NE214 NE231 >HISE2 NE231 0.854 >HISE3 NE248 0.751 0.847 > Start terminus: NH3+ > End terminus: COO- > > --- > Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39 > Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, > line: 583 > > Fatal error: > Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms > while sorting atoms. Maybe different protonation state. > Remove this hydrogen or choose a different protonation state. > Option -ignh will ignore all hydrogens in the input. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence > != HISE) > > Many thanks in advance, > > Alan > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><< > > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the > archive at http://www.gromacs.org/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/mailing_lists/users.php > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa
Hi, This was due to two simultaneous issues. I fixed them both for the next beta release. Note that using HIS iso HISE as a residue name would solve the problem. For 4.5 this should be the normal input, since residue names from the pdb are now preserved. Berk From: alanwil...@gmail.com Date: Mon, 23 Aug 2010 17:45:03 +0100 To: gmx-users@gromacs.org Subject: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa Hi there, I have a system with 'HISE' and using gmx 4.5. ATOM 20 N HISE2 6.376 3.718 -0.053 1.00 0.00 N ATOM 21 H HISE2 5.980 4.646 -0.135 1.00 0.00 H ATOM 22 CA HISE2 7.843 3.744 -0.109 1.00 0.00 C ATOM 23 HA HISE2 8.260 3.319 0.806 1.00 0.00 H ATOM 24 CB HISE2 8.319 2.925 -1.327 1.00 0.00 C ATOM 25 HB2 HISE2 7.855 1.940 -1.312 1.00 0.00 H ATOM 26 HB1 HISE2 7.985 3.435 -2.233 1.00 0.00 H ATOM 27 CG HISE2 9.807 2.703 -1.450 1.00 0.00 C ATOM 28 ND1 HISE2 10.461 2.463 -2.655 1.00 0.00 N ATOM 29 CE1 HISE2 11.770 2.542 -2.382 1.00 0.00 C ATOM 30 HE1 HISE2 12.557 2.484 -3.124 1.00 0.00 H ATOM 31 NE2 HISE2 11.969 2.794 -1.078 1.00 0.00 N ATOM 32 HE2 HISE2 12.817 3.173 -0.672 1.00 0.00 H ATOM 33 CD2 HISE2 10.740 2.839 -0.459 1.00 0.00 C ATOM 34 HD2 HISE2 10.579 3.098 0.574 1.00 0.00 H ATOM 35 C HISE2 8.279 5.228 -0.214 1.00 0.00 C ATOM 36 O HISE2 7.440 6.079 -0.525 1.00 0.00 O when trying: pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none Identified residue HISE1 as a starting terminus. Identified residue HISE3 as a ending terminus.8 out of 8 lines of specbond.dat converted successfullySpecial Atom Distance matrix: HISE1 HISE2 NE214 NE231 HISE2 NE231 0.854 HISE3 NE248 0.751 0.847Start terminus: NH3+End terminus: COO- --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line: 583 Fatal error:Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence != HISE) Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa
Hi there, I have a system with 'HISE' and using gmx 4.5. ATOM 20 N HISE2 6.376 3.718 -0.053 1.00 0.00 N ATOM 21 H HISE2 5.980 4.646 -0.135 1.00 0.00 H ATOM 22 CA HISE2 7.843 3.744 -0.109 1.00 0.00 C ATOM 23 HA HISE2 8.260 3.319 0.806 1.00 0.00 H ATOM 24 CB HISE2 8.319 2.925 -1.327 1.00 0.00 C ATOM 25 HB2 HISE2 7.855 1.940 -1.312 1.00 0.00 H ATOM 26 HB1 HISE2 7.985 3.435 -2.233 1.00 0.00 H ATOM 27 CG HISE2 9.807 2.703 -1.450 1.00 0.00 C ATOM 28 ND1 HISE2 10.461 2.463 -2.655 1.00 0.00 N ATOM 29 CE1 HISE2 11.770 2.542 -2.382 1.00 0.00 C ATOM 30 HE1 HISE2 12.557 2.484 -3.124 1.00 0.00 H ATOM 31 NE2 HISE2 11.969 2.794 -1.078 1.00 0.00 N ATOM 32 HE2 HISE2 12.817 3.173 -0.672 1.00 0.00 H ATOM 33 CD2 HISE2 10.740 2.839 -0.459 1.00 0.00 C ATOM 34 HD2 HISE2 10.579 3.098 0.574 1.00 0.00 H ATOM 35 C HISE2 8.279 5.228 -0.214 1.00 0.00 C ATOM 36 O HISE2 7.440 6.079 -0.525 1.00 0.00 O when trying: pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none Identified residue HISE1 as a starting terminus. Identified residue HISE3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HISE1 HISE2 NE214 NE231 HISE2 NE231 0.854 HISE3 NE248 0.751 0.847 Start terminus: NH3+ End terminus: COO- --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39 Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line: 583 Fatal error: Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence != HISE) Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
