From chemistry-request@server.ccl.net Sun Nov 19 22:59:03 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id WAA14733 for ; Sun, 19 Nov 2000 22:58:58 -0500 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Mon, 20 Nov 2000 12:02:41 +0800 Sender: user@ccl.net Message-ID: <3A18A0A6.2CBAF242@iris.sipp.ac.cn> Date: Mon, 20 Nov 2000 11:55:18 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: problem of add hydrogens using CHARMM Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello: I am a newman in CHARMM program, I met a problem when used it to add hydrogen to a protein molecule. The input file is the following: ------------------------------------- * Generate PSF and CHARMM coordinate set for * the small protein Echistatin * ! Read in Topology and Parameter files open unit 1 card read name top_all22_prot.inp read RTF card unit 1 close unit 1 open unit 1 card read name par_all22_prot.inp read PARA card unit 1 close unit 1 ! Read sequence from the PDB coordinate file open unit 1 card read name 1pef.pdb read sequ pdb unit 1 ! now generate the PSF and also the IC table (SETU keyword) generate prot setu ! read in pdb coordinate file open unit 1 card read name 1pef.pdb read coor pdb unit 1 close unit 1 ! build in hydrogens if using a crystal structure hbuild sele all end ! build in missing coordinates using values in ! the parameter set ic fill ic para ic build ! print all coordinates: undefined coordinates are indicated as ! 9999.00 print coor ! write out the protein structure file (psf) and ! the coordinate file in pdb format. open write formatted unit 27 name 1pef.psf write psf card unit 27 * PSF for echestatin * open unit 1 card write name 1pef-allh.pdb write coor pdb unit 1 * echestatin Structure with hydrogens * close unit 1 stop -------------------------------------------------------- And a part of the output file is the following: =---------------------------------------------- CHARMM> ! Read sequence from the PDB coordinate file CHARMM> open unit 1 card read name 1pef.pdb VOPEN> Attempting to open::1pef.pdb:: OPNLGU> Unit 1 opened for READONLY access to 1pef.pdb CHARMM> read sequ pdb unit 1 MAINIO> Sequence information being read from unit 1. TITLE> * RESIDUE SEQUENCE -- 18 RESIDUES GLU GLN LEU LEU LYS ALA LEU GLU PHE LEU LEU LYS GLU LEU LEU GLU LYS LEU ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 7 TITRATABLE GROUPS THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF HIS - 0 ASP - 0 GLU - 4 LYS - 3 TYR - 0 CHARMM> CHARMM> ! now generate the PSF and also the IC table (SETU keyword) CHARMM> CHARMM> generate prot setu THE PATCH 'NTER ' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CTER ' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is PROT. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 18 Number of atoms = 328 Number of groups = 100 Number of bonds = 328 Number of angles = 609 Number of dihedrals = 882 Number of impropers = 43 Number of HB acceptors = 28 Number of HB donors = 31 Number of NB exclusions = 0 Total charge = -1.00000 CHARMM> CHARMM> ! read in pdb coordinate file CHARMM> open unit 1 card read name 1pef.pdb OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::1pef.pdb:: OPNLGU> Unit 1 opened for READONLY access to 1pef.pdb CHARMM> read coor pdb unit 1 SPATIAL COORDINATES BEING READ FROM UNIT 1 TITLE> * ** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored: SEGID= RESID=1 RESNAME= GLU TYPE= N *** LEVEL 1 WARNING *** BOMLEV IS 0 ** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored: SEGID= RESID=1 RESNAME= GLU TYPE= CA *** LEVEL 1 WARNING *** BOMLEV IS 0 ** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored: SEGID= RESID=1 RESNAME= GLU TYPE= C *** LEVEL 1 WARNING *** BOMLEV IS 0 ** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored: SEGID= RESID=1 RESNAME= GLU TYPE= O *** LEVEL 1 WARNING *** BOMLEV IS 0 ** WARNING ** After reading, there are no coordinates for selected atom: 1 1 GLU N ** WARNING ** After reading, there are no coordinates for selected atom: 2 1 GLU HT1 ** WARNING ** After reading, there are no coordinates for selected atom: 3 1 GLU HT2 ** WARNING ** After reading, there are no coordinates for selected atom: 4 1 GLU HT3 ** WARNING ** After reading, there are no coordinates for selected atom: 5 1 GLU CA ** WARNING ** After reading, there are no coordinates for selected atom: 6 1 GLU HA ** WARNING ** After reading, there are no coordinates for selected atom: 7 1 GLU CB ** WARNING ** After reading, there are no coordinates for selected atom: 8 1 GLU HB1 ** WARNING ** After reading, there are no coordinates for selected atom: 9 1 GLU HB2 ** WARNING ** After reading, there are no coordinates for selected atom: 10 1 GLU CG ** A total of 328 selected atoms have no coordinates ** MESSAGE ** 153 atoms in coordinate file were outside the specified sequence range. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> ! build in hydrogens if using a crystal structure CHARMM> hbuild sele all end SELRPN> 328 atoms have been selected out of 328 PRNHBD: CUToff Hydrogen Bond distance = 0.5000 Angle = 90.0000 CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000 CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000 ACCEptor antecedents included All hydrogen bonds for each hydrogen will be found Hydrogen bonds between excluded atoms will be kept NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 937 exclusions and 879 interactions(1-4) found 291 group exclusions. CUToff Hydrogen Bond distance = 0.5000 Angle = 90.0000 CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000 CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000 ACCEptor antecedents included dihedral PHI STePs for spin = 10.0000 cutoff for water acceptor search CUTWat= 7.5000 WARNING FROM HBUILD: Attempt to construct a hydrogen bonded to the atom PROT 1 GLU N with unknown coordinates. *** LEVEL 0 WARNING *** BOMLEV IS 0 BOMLEV HAS BEEN SATISFIED. TERMINATING. ===================================================================================================== I wish you can help me solve this problem. Thanks. Regards, mao xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~