From owner-nwchem-users@emsl.pnl.gov Thu May 17 12:54:10 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l4HJs9EH020608 for ; Thu, 17 May 2007 12:54:10 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l4HJs9p3020607 for nwchem-users-outgoing-0915; Thu, 17 May 2007 12:54:09 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Possible-Spoof: True X-IronPort-AV: i="4.14,549,1170662400"; d="scan'208"; a="20456112:sNHT61826149" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: RE: [NWCHEM] Problem with Reading my PDB File Date: Thu, 17 May 2007 12:54:06 -0700 Message-ID: In-Reply-To: <63568.69.134.73.57.1179430404.squirrel@webmail.ncsu.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] Problem with Reading my PDB File thread-index: AceYutAiC2P2/oBgSVGjK7yw9h2ufwAAY40g References: <63568.69.134.73.57.1179430404.squirrel@webmail.ncsu.edu> From: "Venkatnathan, Arun" To: "Naomi Caldwell" , X-OriginalArrivalTime: 17 May 2007 19:54:07.0201 (UTC) FILETIME=[20ED4510:01C798BD] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id l4HJs8Po020604 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Hi, See line 2 of your first prepare script. The words "system cnt_md" is missing in the script. You may need a cnt.frg (this is a fragment file) file. That may resolve your problem. - Arun - -----Original Message----- From: owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Naomi Caldwell Sent: Thursday, May 17, 2007 12:33 PM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] Problem with Reading my PDB File Hey, I have been attempting to use nwchem for molecular dynamics on a carbon nanotube. The beginning example in the tutorial using et10.pdb runs okay, and, as far as I can tell, my pdb file uses the same format. Could any of you possibly tell me why it fails? The nw and pdb files are listed below. The error I get is: ----------------------------------------------------------- Unresolved atom types in fragment cnt ********** * 0: pre_mkfrg failed 9999 ********** 0:0::: 9999 0:0::: 9999 Last System Error Message from Task 0:: Inappropriate ioctl for device 0: ARMCI aborting 9999 (0x270f). 0: ARMCI aborting 9999 (0x270f). system error message: Inappropriate ioctl for device ------------------------------------------------------------ The pdb file is: ----------------- title "Prepare QM/MM calculation of ethanol" start cnt prepare source mod_nano.pdb new_top new_seq new_rst center solvate box 1.0 2.0 3.0 end md system cnt_md end task prepare -------------------------------------------------------------- The pdb file is: ---------------- ATOM 1 C cnt 1 0.000 0.000 0.000 1.00 0.00 C ATOM 2 C cnt 1 1.445 0.000 0.000 1.00 0.00 C ATOM 3 C cnt 1 2.132 1.216 0.000 1.00 0.00 C ATOM 4 C cnt 1 1.391 2.455 0.016 1.00 0.00 C ATOM 5 C cnt 1 0.107 2.387 -0.570 1.00 0.00 C ATOM 6 C cnt 1 -0.600 1.142 -0.570 1.00 0.00 C ATOM 7 C cnt 1 3.547 0.442 -1.787 1.00 0.00 C ATOM 8 C cnt 1 3.893 1.067 -3.039 1.00 0.00 C ATOM 9 C cnt 1 2.845 -0.805 -1.789 1.00 0.00 C ATOM 10 C cnt 1 2.935 0.796 -4.082 1.00 0.00 C ATOM 11 C cnt 1 2.487 -1.419 -3.048 1.00 0.00 C ATOM 12 C cnt 1 2.232 -0.450 -4.089 1.00 0.00 C ATOM 13 C cnt 1 2.000 -1.130 -0.708 1.00 0.00 C ATOM 14 C cnt 1 3.394 1.322 -0.693 1.00 0.00 C ATOM 15 C cnt 1 -0.150 3.352 -1.609 1.00 0.00 C ATOM 16 C cnt 1 -1.559 0.869 -1.616 1.00 0.00 C ATOM 17 C cnt 1 -0.505 2.740 -2.864 1.00 0.00 C ATOM 18 C cnt 1 -1.213 1.497 -2.870 1.00 0.00 C ATOM 19 C cnt 1 0.332 3.067 -3.955 1.00 0.00 C ATOM 20 C cnt 1 -1.055 0.610 -3.956 1.00 0.00 C ATOM 21 C cnt 1 0.891 1.933 -4.652 1.00 0.00 C ATOM 22 C cnt 1 0.202 0.719 -4.659 1.00 0.00 C ATOM 23 C cnt 1 2.335 1.935 -4.664 1.00 0.00 C ATOM 24 C cnt 1 0.945 -0.520 -4.663 1.00 0.00 C ATOM 25 C cnt 1 1.045 4.307 -3.948 1.00 0.00 C ATOM 26 C cnt 1 3.035 3.182 -4.652 1.00 0.00 C ATOM 27 C cnt 1 2.296 4.412 -4.641 1.00 0.00 C ATOM 28 C cnt 1 0.558 4.565 -1.610 1.00 0.00 C ATOM 29 C cnt 1 0.900 5.193 -2.856 1.00 0.00 C ATOM 30 C cnt 1 4.319 3.261 -4.066 1.00 0.00 C ATOM 31 C cnt 1 4.569 2.298 -3.030 1.00 0.00 C ATOM 32 C cnt 1 2.996 5.642 -4.630 1.00 0.00 C ATOM 33 C cnt 1 5.018 4.515 -4.053 1.00 0.00 C ATOM 34 C cnt 1 4.418 5.644 -4.650 1.00 0.00 C ATOM 35 C cnt 1 2.440 6.761 -3.950 1.00 0.00 C ATOM 36 C cnt 1 1.619 6.437 -2.850 1.00 0.00 C ATOM 37 C cnt 1 2.101 3.697 0.012 1.00 0.00 C ATOM 38 C cnt 1 1.509 4.841 -0.570 1.00 0.00 C ATOM 39 C cnt 1 1.985 7.022 -1.612 1.00 0.00 C ATOM 40 C cnt 1 2.226 6.086 -0.575 1.00 0.00 C ATOM 41 C cnt 1 4.928 2.908 -1.780 1.00 0.00 C ATOM 42 C cnt 1 4.091 2.572 -0.692 1.00 0.00 C ATOM 43 C cnt 1 5.942 4.785 -3.012 1.00 0.00 C ATOM 44 C cnt 1 5.625 4.165 -1.778 1.00 0.00 C ATOM 45 C cnt 1 3.535 3.695 0.005 1.00 0.00 C ATOM 46 C cnt 1 3.501 6.148 0.026 1.00 0.00 C ATOM 47 C cnt 1 4.231 4.928 0.002 1.00 0.00 C ATOM 48 C cnt 1 5.478 5.031 -0.674 1.00 0.00 C ATOM 49 C cnt 1 -0.706 -1.244 -0.003 1.00 0.00 C ATOM 50 C cnt 1 1.296 -2.376 -0.711 1.00 0.00 C ATOM 51 C cnt 1 0.036 -2.485 -0.011 1.00 0.00 C ATOM 52 C cnt 1 -1.991 -1.314 -0.579 1.00 0.00 C ATOM 53 C cnt 1 -2.249 -0.344 -1.619 1.00 0.00 C ATOM 54 C cnt 1 -2.604 -0.960 -2.878 1.00 0.00 C ATOM 55 C cnt 1 -1.761 -0.634 -3.960 1.00 0.00 C ATOM 56 C cnt 1 0.240 -1.766 -4.668 1.00 0.00 C ATOM 57 C cnt 1 -1.205 -1.767 -4.664 1.00 0.00 C ATOM 58 C cnt 1 1.802 -2.634 -3.052 1.00 0.00 C ATOM 59 C cnt 1 0.840 -2.907 -4.096 1.00 0.00 C ATOM 60 C cnt 1 1.453 -3.261 -1.798 1.00 0.00 C ATOM 61 C cnt 1 -0.652 -3.699 -0.017 1.00 0.00 C ATOM 62 C cnt 1 -0.095 -4.832 -0.719 1.00 0.00 C ATOM 63 C cnt 1 0.748 -4.506 -1.802 1.00 0.00 C ATOM 64 C cnt 1 0.135 -4.151 -4.099 1.00 0.00 C ATOM 65 C cnt 1 0.397 -5.121 -3.061 1.00 0.00 C ATOM 66 C cnt 1 -2.097 -3.701 -0.010 1.00 0.00 C ATOM 67 C cnt 1 -2.696 -2.559 -0.584 1.00 0.00 C ATOM 68 C cnt 1 -3.309 -2.205 -2.881 1.00 0.00 C ATOM 69 C cnt 1 -3.659 -2.828 -1.626 1.00 0.00 C ATOM 70 C cnt 1 -1.892 -2.982 -4.666 1.00 0.00 C ATOM 71 C cnt 1 -3.153 -3.090 -3.968 1.00 0.00 C ATOM 72 C cnt 1 -1.150 -4.222 -4.676 1.00 0.00 C ATOM 73 C cnt 1 -4.344 -4.045 -1.631 1.00 0.00 C ATOM 74 C cnt 1 -4.706 -4.656 -2.888 1.00 0.00 C ATOM 75 C cnt 1 -1.857 -5.467 -4.677 1.00 0.00 C ATOM 76 C cnt 1 -3.855 -4.337 -3.970 1.00 0.00 C ATOM 77 C cnt 1 -3.299 -5.467 -4.671 1.00 0.00 C ATOM 78 C cnt 1 -1.250 -6.610 -4.112 1.00 0.00 C ATOM 79 C cnt 1 -0.295 -6.334 -3.064 1.00 0.00 C ATOM 80 C cnt 1 -0.803 -6.076 -0.725 1.00 0.00 C ATOM 81 C cnt 1 -0.636 -6.965 -1.810 1.00 0.00 C ATOM 82 C cnt 1 -2.060 -6.183 -0.028 1.00 0.00 C ATOM 83 C cnt 1 -2.801 -4.947 -0.018 1.00 0.00 C ATOM 84 C cnt 1 -4.093 -5.011 -0.587 1.00 0.00 C ATOM 85 C cnt 1 -3.986 -6.691 -4.657 1.00 0.00 C ATOM 86 C cnt 1 -5.405 -5.904 -2.886 1.00 0.00 C ATOM 87 C cnt 1 -5.241 -6.801 -3.967 1.00 0.00 C ATOM 88 C cnt 1 -3.251 -7.926 -4.671 1.00 0.00 C ATOM 89 C cnt 1 -1.957 -7.853 -4.106 1.00 0.00 C ATOM 90 C cnt 1 -1.702 -8.812 -3.071 1.00 0.00 C ATOM 91 C cnt 1 -1.347 -8.206 -1.820 1.00 0.00 C ATOM 92 C cnt 1 -2.203 -8.532 -0.743 1.00 0.00 C ATOM 93 C cnt 1 -2.757 -7.402 -0.049 1.00 0.00 C ATOM 94 C cnt 1 -4.795 -6.257 -0.600 1.00 0.00 C ATOM 95 C cnt 1 -5.746 -6.526 -1.640 1.00 0.00 C ATOM 96 C cnt 1 -4.194 -7.407 -0.039 1.00 0.00 C ATOM 97 C cnt 1 -6.437 -7.761 -1.646 1.00 0.00 C ATOM 98 C cnt 1 -6.195 -8.708 -0.613 1.00 0.00 C ATOM 99 C cnt 1 -4.899 -8.658 -0.056 1.00 0.00 C ATOM 100 C cnt 1 -6.801 -8.358 -2.884 1.00 0.00 C ATOM 101 C cnt 1 -5.941 -8.055 -3.961 1.00 0.00 C ATOM 102 C cnt 1 -5.378 -9.168 -4.634 1.00 0.00 C ATOM 103 C cnt 1 -3.961 -9.175 -4.662 1.00 0.00 C ATOM 104 C cnt 1 -4.165 -9.869 -0.089 1.00 0.00 C ATOM 105 C cnt 1 -2.919 -9.777 -0.757 1.00 0.00 C ATOM 106 C cnt 1 -2.405 -10.040 -3.072 1.00 0.00 C ATOM 107 C cnt 1 -3.340 -10.315 -4.109 1.00 0.00 C ATOM 108 C cnt 1 -2.734 -10.665 -1.838 1.00 0.00 C END --------------------------------------------------------------------- Thanks! - Naomi Caldwell