From owner-nwchem-users@emsl.pnl.gov Tue Feb 1 16:06:12 2005 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.12.10/8.12.10) with ESMTP id j1206Cmp007900 for ; Tue, 1 Feb 2005 16:06:12 -0800 (PST) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.12.10/8.12.10/Submit) id j1206CVh007899 for nwchem-users-outgoing; Tue, 1 Feb 2005 16:06:12 -0800 (PST) Date: Tue, 01 Feb 2005 18:06:07 -0600 From: Glenn Johnson Subject: Using glycam_93 with NWChem-4.6 To: nwchem-users@emsl.pnl.gov Message-id: <4200196F.7000406@srrc.ars.usda.gov> Organization: USDA, ARS, SRRC MIME-version: 1.0 Content-type: multipart/mixed; boundary=------------030707050100040900060805 X-Accept-Language: en-us, en User-Agent: Mozilla Thunderbird 1.0 (X11/20041208) X-Enigmail-Version: 0.89.5.0 X-Enigmail-Supports: pgp-inline, pgp-mime Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk This is a multi-part message in MIME format. --------------030707050100040900060805 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit I would like to use the glycam_93 force field to do MD simulations of cellobiose with NWChem-4.6 but I am not able to get my topology files generated. Could someone please take a look at the attached input/output files and see if I have anything blatantly wrong? Thanks. -- Glenn Johnson U.S. Department of Agriculture Agricultural Research Service Southern Regional Research Center New Orleans, LA --------------030707050100040900060805 Content-Type: text/x-log; name="cellobiose.log" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="cellobiose.log" argument 1 = cellobiose.nw Northwest Computational Chemistry Package (NWChem) 4.6 ------------------------------------------------------ Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland, WA 99352 COPYRIGHT (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004 Pacific Northwest National Laboratory, Battelle Memorial Institute. >>> All Rights Reserved <<< DISCLAIMER ---------- This material was prepared as an account of work sponsored by an agency of the United States Government. 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Job information --------------- hostname = node1 program = nwchem date = Tue Feb 1 17:01:19 2005 compiled = Fri Aug 27 13:57:52 CDT 2004 source = /home/glenn/nwchem/nwchem-4.6_intel_atlas nwchem branch = 4.6 input = cellobiose.nw prefix = cellobiose. data base = ./cellobiose.db status = startup nproc = 1 time left = -1s Memory information ------------------ heap = 39321594 doubles = 300.0 Mbytes stack = 13107187 doubles = 100.0 Mbytes global = 52428804 doubles = 400.0 Mbytes (within heap+stack) total = 52428781 doubles = 400.0 Mbytes verify = yes hardfail = no Directory information --------------------- 0 permanent = . 0 scratch = /usr/scratch NWChem Input Module ------------------- Prepare Module -------------- Force field amber Directories used for fragment and segment files /usr/local/NWChem/data/amber_s/ /usr/local/NWChem/data/amber_q/ /usr/local/NWChem/data/amber_x/ /usr/local/NWChem/data/amber_u/ ./ Parameter files used to resolve force field parameters /usr/local/NWChem/data/amber_s/amber.par /usr/local/NWChem/data/amber_q/amber.par /usr/local/NWChem/data/amber_x/glycam.par /usr/local/NWChem/data/amber_u/amber.par ./amber.par PDB geometry cellobiose.pdb Created sequence ./cellobiose.seq Parameter file /usr/local/NWChem/data/amber_s/amber.par Parameter file /usr/local/NWChem/data/amber_q/amber.par Parameter file /usr/local/NWChem/data/amber_x/glycam.par Undetermined force field parameters Parameters could not be found for angle type H2 -CT -OH ( H3 - C2 - O2 )UNK 1 15 2 36 10 1 0 Parameters could not be found for angle type OH -CT -OS ( O2 - C2 - O9 )UNK 1 36 2 43 12 1 0 ****************************************************************************************************** * 0: pre_check failed 9999 * ****************************************************************************************************** 0:0::: 9999 p0_15149: p4_error: : 9999 --------------030707050100040900060805 Content-Type: text/plain; name="cellobiose.nw" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="cellobiose.nw" prepare system cellobiose source pdb end task prepare --------------030707050100040900060805 Content-Type: text/plain; name="cellobiose.pdb" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="cellobiose.pdb" REMARK 888 REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC) MODEL 1 HETATM 1 CT1 UNK0 1 2.723 -0.534 2.677 1.00 0.00 C HETATM 2 CT2 UNK0 1 0.491 3.484 0.090 1.00 0.00 C HETATM 3 CT3 UNK0 1 2.909 -2.035 2.486 1.00 0.00 C HETATM 4 CT4 UNK0 1 1.867 3.663 0.695 1.00 0.00 C HETATM 5 CT5 UNK0 1 3.558 -2.599 3.739 1.00 0.00 C HETATM 6 CT6 UNK0 1 2.522 2.308 0.908 1.00 0.00 C HETATM 7 CT7 UNK0 1 4.886 -1.876 3.997 1.00 0.00 C HETATM 8 CT8 UNK0 1 1.601 1.343 1.657 1.00 0.00 C HETATM 9 CT9 UNK0 1 4.693 -0.356 3.995 1.00 0.00 C HETATM 10 CT10 UNK0 1 0.191 1.313 1.070 1.00 0.00 C HETATM 11 CT11 UNK0 1 6.032 0.361 3.967 1.00 0.00 C HETATM 12 CT12 UNK0 1 -0.798 0.572 1.920 1.00 0.00 C HETATM 13 OG1 UNK0 1 2.123 0.000 1.534 1.00 0.00 O HETATM 14 OH1 UNK0 1 -0.151 4.701 -0.004 1.00 0.00 O HETATM 15 OH2 UNK0 1 1.670 -2.642 2.165 1.00 0.00 O HETATM 16 OH3 UNK0 1 2.714 4.384 -0.192 1.00 0.00 O HETATM 17 OH4 UNK0 1 3.739 -4.012 3.660 1.00 0.00 O HETATM 18 OH5 UNK0 1 3.735 2.535 1.589 1.00 0.00 O HETATM 19 OH6 UNK0 1 5.374 -2.287 5.265 1.00 0.00 O HETATM 20 OS1 UNK0 1 4.010 0.064 2.803 1.00 0.00 O HETATM 21 OS2 UNK0 1 -0.302 2.657 0.953 1.00 0.00 O HETATM 22 OH7 UNK0 1 5.891 1.746 3.701 1.00 0.00 O HETATM 23 OH8 UNK0 1 -2.026 0.354 1.236 1.00 0.00 O HETATM 24 HC1 UNK0 1 2.198 -0.326 3.512 1.00 0.00 H HETATM 25 HO1 UNK0 1 -0.425 4.828 -0.942 1.00 0.00 H HETATM 26 HC2 UNK0 1 0.618 3.197 -0.977 1.00 0.00 H HETATM 27 HO2 UNK0 1 1.185 -2.792 3.019 1.00 0.00 H HETATM 28 HC3 UNK0 1 3.487 -2.218 1.629 1.00 0.00 H HETATM 29 HC4 UNK0 1 1.787 4.149 1.603 1.00 0.00 H HETATM 30 HO3 UNK0 1 2.378 5.128 -0.585 1.00 0.00 H HETATM 31 HO4 UNK0 1 4.150 -4.071 2.871 1.00 0.00 H HETATM 32 HC5 UNK0 1 2.899 -2.349 4.403 1.00 0.00 H HETATM 33 HC6 UNK0 1 2.798 1.827 0.000 1.00 0.00 H HETATM 34 HO5 UNK0 1 4.084 1.827 2.138 1.00 0.00 H HETATM 35 HO6 UNK0 1 6.343 -2.544 5.233 1.00 0.00 H HETATM 36 HC7 UNK0 1 5.549 -2.218 3.258 1.00 0.00 H HETATM 37 HC8 UNK0 1 1.498 1.566 2.622 1.00 0.00 H HETATM 38 HC9 UNK0 1 4.155 0.065 4.795 1.00 0.00 H HETATM 39 HC10 UNK0 1 0.327 0.848 0.127 1.00 0.00 H HETATM 40 HO7 UNK0 1 5.914 2.218 4.510 1.00 0.00 H HETATM 41 HO8 UNK0 1 -2.538 1.096 1.018 1.00 0.00 H HETATM 42 HC11 UNK0 1 6.646 -0.026 3.258 1.00 0.00 H HETATM 43 HC12 UNK0 1 -0.347 1.044 2.749 1.00 0.00 H HETATM 44 HC13 UNK0 1 -0.307 -0.261 2.240 1.00 0.00 H HETATM 45 HC14 UNK0 1 6.402 0.000 4.938 1.00 0.00 H CONECT 1 3 13 20 24 CONECT 2 4 14 21 26 CONECT 3 1 5 15 28 CONECT 4 2 6 16 29 CONECT 5 3 7 17 32 CONECT 6 4 8 18 33 CONECT 7 5 9 19 36 CONECT 8 6 10 13 37 CONECT 9 7 11 20 38 CONECT 10 8 12 21 39 CONECT 11 9 22 42 45 CONECT 12 10 23 43 44 CONECT 13 1 8 CONECT 14 2 25 CONECT 15 3 27 CONECT 16 4 30 CONECT 17 5 31 CONECT 18 6 34 CONECT 19 7 35 CONECT 20 1 9 CONECT 21 2 10 CONECT 22 11 40 CONECT 23 12 41 CONECT 24 1 CONECT 25 14 CONECT 26 2 CONECT 27 15 CONECT 28 3 CONECT 29 4 CONECT 30 16 CONECT 31 17 CONECT 32 5 CONECT 33 6 CONECT 34 18 CONECT 35 19 CONECT 36 7 CONECT 37 8 CONECT 38 9 CONECT 39 10 CONECT 40 22 CONECT 41 23 CONECT 42 11 CONECT 43 12 CONECT 44 12 CONECT 45 11 ENDMDL END --------------030707050100040900060805--