The pdb file for formic acid is:
ATOM 1 C FORH 1 -4.360 0.340 -0.050 0.00 0.00 ATOM 2 H FORH 1 -5.450 0.260 -0.050 0.00 0.00 ATOM 3 O2 FORH 1 -3.790 1.370 -0.050 0.00 0.00 ATOM 4 O1 FORH 1 -3.730 -0.830 -0.050 0.00 0.00 ATOM 5 HO1 FORH 1 -4.350 -1.550 -0.050 0.00 0.00 The output of the pdb2gmx is: GROMACS: gmx pdb2gmx, VERSION 5.1.4 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx pdb2gmx -f formic-acid.pdb -ter Select the Force Field: From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: CHARMM36 all-atom force field (November 2018) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 9 Using the Charmm36-nov2018 force field in directory charmm36-nov2018.ff Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None 6 Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.r2b Reading formic-acid.pdb... Read 5 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 5 atoms chain #res #atoms 1 'X' 1 5 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/atomtypes.atp Atomtype 447 Reading residue database... (charmm36-nov2018) Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.rtp Residue 1318 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.c.tdb Back Off! I just backed up topol.top to ./#topol.top.1# Processing chain 1 'X' (5 atoms, 1 residues) Warning: Starting residue FORH1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /usr/local/gromacs/share/gromacs/top/charmm36-nov2018.ff/merged.arn ------------------------------------------------------- Program gmx pdb2gmx, VERSION 5.1.4 Source code file: /home/chengqianwei/program/gromacs-5.1.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 746 Fatal error: Atom HN in residue FORH 1 was not found in rtp entry FORH with 5 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. 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 From: Justin Lemkul <jalem...@vt.edu> Date: 2019-03-29 09:16:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to create top of small molecules with pdb2gmx> > >On 3/28/19 9:03 PM, Tingguang.S wrote: >> Thank you Justin, >> >> >> I had tried many times, and the interactive selection still didn't work, I >> really need help. I downloaded charmm36-nov2018.ff.tgz from >> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs, and extracted it >> into /usr/local/gromacs/share/gromacs/top. >> >> >> I had attached the log file, and pdb file of formic acid. Please help with >> this. > >The mailing list does not accept attachments. Please post files to a >file-sharing service and provide a URL. > >-Justin > >> >> Thank you for your time! >> >> >> >> >> 发件人：Justin Lemkul <jalem...@vt.edu> >> 发送日期：2019-03-28 21:48:32 >> 收件人：gmx-us...@gromacs.org >> 主题：Re: [gmx-users] How to create top of small molecules with pdb2gmx> >>> On 3/28/19 9:36 AM, Tingguang.S wrote: >>>> Thank you, Justin！ >>>> >>>> >>>> You mean that I should use the following command: "gmx pdb2gmx -f >>>> formic-acid.pdb -ter "？ >>>> I had used the flag -ter, but the program did not prompt interactive >>>> selection. >>> I don't know how that could have happened. The purpose of -ter is to >>> trigger an interactive selection. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Office: 301 Fralin Hall >>> Lab: 303 Engel Hall >>> >>> Virginia Tech Department of Biochemistry >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.thelemkullab.com >>> >>> ================================================== >>> >>> -- >>> 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. >Assistant Professor >Office: 301 Fralin Hall >Lab: 303 Engel Hall > >Virginia Tech Department of Biochemistry >340 West Campus Dr. >Blacksburg, VA 24061 > >jalem...@vt.edu | (540) 231-3129 >http://www.thelemkullab.com > >================================================== > >-- >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.
