Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN
On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN
Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN
Well... that was a rookie mistake. Sorry about that. Thank you! Il giorno gio 20 ago 2015 alle ore 14:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 8:16 AM, Simone Bolognini wrote: Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. pdb2gmx -ignh -Justin Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN
On 8/20/15 8:16 AM, Simone Bolognini wrote: Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. pdb2gmx -ignh -Justin Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! No, you can't copy and paste, because then you're mixing force fields and that is bad practice. HSD is just delta-protonated HIS, which is already in AMBER. It's just called HID, so rename your coordinate files appropriately and you can generate the topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Adding HSD residue to AMBER ff99SB-ILDN
Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue database. I looked at the source files and found out that CHARMM has it. In particular, this is what you can find in the CHARMM database: [ HSD ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 -0.09 4 HB1 HA 0.09 5 HB2 HA 0.09 6 ND1 NR1 -0.36 7 HD1 H 0.32 8 CG CPH1 -0.05 9 CE1 CPH2 0.25 10 HE1 HR1 0.13 11 NE2 NR2 -0.70 12 CD2 CPH1 0.22 13 HD2 HR3 0.10 14 C C 0.51 15 O O -0.51 16 [ bonds ] CB CA CG CB ND1 CG CE1 ND1 NE2 CD2 N HN N CA C CA C +N CA HA CB HB1 CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 O C CG CD2 CE1 NE2 [ impropers ] ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 N -C CA HN C CA +N O [ cmap ] -C N CA C +N Is there any possible way in which I can copy and paste this in the Amber database and hope it will work correctly? Thank you very much!!! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
