VMD-L Mailing List
From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Sat Sep 20 2008 - 09:47:50 CDT
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i am using the command
$package require solvate
$solvate aoq.psf aoq.pdb -t 10 -o aoq_wb
this type of command is working for other molecule but this time its breaking.
as for my os is ocncerned:
Linux snbpc30.lan.bose.res.in 2.6.25.14-69.fc8 #1 SMP Mon Aug 4 14:20:24 EDT 2008 i686 i686 i386 GNU/Linux.
-- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html ----- Original Message ---- From: John Stone <johns_at_ks.uiuc.edu> To: Rudra Banerjee <bnrj.rudra_at_yahoo.com> Cc: vmd-l_at_ks.uiuc.edu Sent: Saturday, 20 September, 2008 12:42:59 PM Subject: Re: vmd-l: solvate a molecule Hi, What commands are you issuing in order to solvate your structure? We'll also need to know what OS and hardware platform you're using. Cheers, John Stone vmd_at_ks.uiuc.edu On Sat, Sep 20, 2008 at 11:38:03AM +0530, Rudra Banerjee wrote: > i have managed to create a non-std molecule (acridine orange) . now the proble is when i am trying th solvate it in water using vmd(Tk console), the vmd is crashing without giving any error /log. hence i am not getting any clue about what is going wrong.plz help.. > my pdb file is: > REMARK original generated coordinate pdb file > ATOM 1 C MAC 0 0.000 0..000 0.000 -1.00 0.00 U C > ATOM 2 OT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O > ATOM 3 OT2 MAC 0 0.000 0.000 0.000 -1..00 0.00 U O > ATOM 4 N MAC 0 0.123 -0.642 0.571 1.00 0.00 U N > ATOM 5 HT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H > ATOM 6 HT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H > ATOM 7 HT3 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H > ATOM 8 CA MAC 0 -5.107 1.352 1.005 1.00 0.00 U C > ATOM 9 HA MAC 0 0.000 0.000 0.000 -1.00 0.00 U H > ATOM 10 N2 MAC 0 -4.299 0.713 1.207 1.00 0..00 U N > ATOM 11 HA1 MAC 0 -5.986 1.045 1.614 1..00 0.00 U H > ATOM 12 HA2 MAC 0 -4.830 2.397 1.270 1.00 0.00 U H > ATOM 13 HA3 MAC 0 -5.354 1.307 -0..080 1.00 0.00 U H > ATOM 14 CB MAC 0 -4.392 -0..073 1.897 1.00 0.00 U C > ATOM 15 HB1 MAC 0 -3..663 0.071 2.725 1.00 0.00 U H > ATOM 16 HB2 MAC 0 -5.425 -0.085 2.310 1.00 0.00 U H > ATOM 17 HB3 MAC 0 -4.187 -1.041 1.386 1.00 0.00 U H > ATOM 18 CD1 MAC 0 -3.039 1.934 -0.283 1.00 0.00 U C > ATOM 19 HD1 MAC 0 -3.879 2.612 -0.492 1.00 0.00 U H > ATOM 20 CE1 MAC 0 -1.812 2.120 -0.917 1.00 0.00 U C > ATOM 21 HE1 MAC 0 -1.685 2.949 -1.629 1.00 0.00 U H > ATOM 22 CZ MAC 0 -0.733 1.261 -0.643 1.00 0.00 U C > ATOM 23 CG MAC 0 -3.189 0.892 0.625 1.00 0.00 U C > ATOM 24 CD2 MAC 0 -2.112 0.042 0.894 1.00 0.00 U C > ATOM 25 HD2 MAC 0 -2.248 -0.784 1.607 1.00 0.00 U H > ATOM 26 CE2 MAC 0 -0.879 0..204 0.276 1.00 0.00 U C > ATOM 27 C1 MAC 0 0.512 1.419 -1.262 1.00 0.00 U C > ATOM 28 H1 MAC 0 0.669 2.239 -1.978 1.00 0.00 U H > ATOM 29 C2 MAC 0 1.562 0.544 -0.962 1.00 0.00 U C > ATOM 30 C3 MAC 0 1.315 -0.482 -0.029 1.00 0.00 U C > ATOM 31 C4 MAC 0 2.827 0.670 -1.563 1.00 0.00 U C > ATOM 32 H4 MAC 0 3.013 1.474 -2.290 1.00 0.00 U H > ATOM 33 C5 MAC 0 3.854 -0.212 -1.232 1.00 0.00 U C > ATOM 34 H5 MAC 0 4.846 -0.106 -1.696 1.00 0.00 U H > ATOM 35 C7 MAC 0 2.353 -1.354 0.273 1.00 0..00 U C > ATOM 36 H7 MAC 0 2.175 -2.167 0.992 1..00 0.00 U H > ATOM 37 C6 MAC 0 3.613 -1.234 -0.321 1.00 0.00 U C > ATOM 38 N1 MAC 0 4.671 -2.189 0.006 1.00 0.00 U N > ATOM 39 C8 MAC 0 5.628 -2.116 -0.419 1.00 0.00 U C > ATOM 40 C9 MAC 0 4.407 -3.273 0.925 1.00 0.00 U C > ATOM 41 H81 MAC 0 6.081 -1.136 -0.148 1.00 0.00 U H > ATOM 42 H82 MAC 0 5.550 -2.185 -1.527 1.00 0.00 U H > ATOM 43 H83 MAC 0 6.270 -2.939 -0.032 1.00 0.00 U H > ATOM 44 H91 MAC 0 4.096 -2.858 1.910 1.00 0.00 U H > ATOM 45 H92 MAC 0 5.323 -3.895 1.040 1.00 0.00 U H > ATOM 46 H93 MAC 0 3.586 -3.909 0.524 1.00 0.00 U H > END > > and here is the corresponding psf file is: > > > PSF > > 6 !NTITLE > REMARKS original generated structure x-plor psf file > REMARKS 2 patches were applied to the molecule. > REMARKS topology my-top.inp > REMARKS segment U { first NTER; last CTER; auto angles dihedrals } > REMARKS defaultpatch NTER U:A 1 > REMARKS defaultpatch CTER U:A 1 > > 46 !NATOM > 1 U A 1 MAC C CC 0.340000 12.0110 0 > 2 U A 1 MAC OT1 OC -0.670000 15.9990 0 > 3 U A 1 MAC OT2 OC -0.670000 15.9990 0 > 4 U A 1 MAC N NH3 -0.300000 14.0070 0 > 5 U A 1 MAC HT1 HC 0.330000 1.0080 0 > 6 U A 1 MAC HT2 HC 0.330000 1.0080 0 > 7 U A 1 MAC HT3 HC 0.330000 1.0080 0 > 8 U A 1 MAC CA CT1 0.210000 12.0110 0 > 9 U A 1 MAC HA HB 0.100000 1.0080 0 > 10 U A 1 MAC N2 NH2 -0.470000 14.0070 0 > 11 U A 1 MAC HA1 HB 0.310000 1.0080 0 > 12 U A 1 MAC HA2 HB 0.090000 1.0080 0 > 13 U A 1 MAC HA3 HB 0.000000 1.0080 0 > 14 U A 1 MAC CB CA -0.180000 12.0110 0 > 15 U A 1 MAC HB1 HB 0.090000 1.0080 0 > 16 U A 1 MAC HB2 HB 0.090000 1.0080 0 > 17 U A 1 MAC HB3 HB 0.000000 1.0080 0 > 18 U A 1 MAC CD1 CA -0.115000 12.0110 0 > 19 U A 1 MAC HD1 HP 0.115000 1.0080 0 > 20 U A 1 MAC CE1 CA -0.115000 12.0110 0 > 21 U A 1 MAC HE1 HP 0.115000 1.0080 0 > 22 U A 1 MAC CZ CA 0.000000 12.0110 0 > 23 U A 1 MAC CG CA 0.000000 12.0110 0 > 24 U A 1 MAC CD2 CA -0.115000 12.0110 0 > 25 U A 1 MAC HD2 HP 0.115000 1.0080 0 > 26 U A 1 MAC CE2 CA 0.470000 12.0110 0 > 27 U A 1 MAC C1 CA -0.115000 12.0110 0 > 28 U A 1 MAC H1 HP 0.115000 1.0080 0 > 29 U A 1 MAC C2 CA 0.000000 12.0110 0 > 30 U A 1 MAC C3 CA 0.000000 12.0110 0 > 31 U A 1 MAC C4 CA -0.115000 12.0110 0 > 32 U A 1 MAC H4 HP 0.115000 1.0080 0 > 33 U A 1 MAC C5 CA -0.115000 12.0110 0 > 34 U A 1 MAC H5 HP 0.115000 1.0080 0 > 35 U A 1 MAC C7 CA -0.115000 12.0110 0 > 36 U A 1 MAC H7 HP 0.115000 1.0080 0 > 37 U A 1 MAC C6 CA 0.070000 12.0110 0 > 38 U A 1 MAC N1 NH2 -0.047000 14.0070 0 > 39 U A 1 MAC C8 CA 0.080000 12.0110 0 > 40 U A 1 MAC C9 CA 0.080000 12.0110 0 > 41 U A 1 MAC H81 HB 0.040000 1.0080 0 > 42 U A 1 MAC H82 HB 0.040000 1.0080 0 > 43 U A 1 MAC H83 HB 0.040000 1.0080 0 > 44 U A 1 MAC H91 HB 0.040000 1.0080 0 > 45 U A 1 MAC H92 HB 0.040000 1.0080 0 > 46 U A 1 MAC H93 HB 0.040000 1.0080 0 > > 46 !NBOND: bonds > 1 3 1 2 5 4 6 4 > 7 4 8 11 8 12 8 13 > 10 23 10 8 10 14 14 15 > 14 16 14 17 18 19 18 20 > 20 22 20 21 22 27 22 26 > 23 18 23 24 24 25 26 24 > 26 4 27 28 27 29 29 30 > 29 31 30 4 31 32 31 33 > 33 37 33 34 35 36 35 30 > 37 35 38 37 38 39 38 40 > 39 41 39 42 39 43 40 44 > 40 45 40 46 > > 80 !NTHETA: angles > 3 1 2 4 26 22 5 4 30 > 5 4 26 5 4 7 5 4 6 > 6 4 30 6 4 26 6 4 7 > 7 4 30 7 4 26 8 10 14 > 10 23 24 10 14 17 10 14 16 > 10 14 15 10 8 13 10 8 12 > 10 8 11 11 8 13 11 8 12 > 12 8 13 15 14 17 15 14 16 > 16 14 17 18 23 24 18 23 10 > 19 18 20 20 22 26 20 22 27 > 21 20 18 22 27 29 22 27 28 > 22 20 18 22 20 21 23 18 20 > 23 18 19 23 10 14 23 10 8 > 24 26 22 24 26 4 25 24 23 > 26 24 23 26 24 25 26 4 30 > 27 22 26 28 27 29 29 31 33 > 29 31 32 29 30 4 29 30 35 > 30 35 37 30 29 27 30 29 31 > 31 29 27 32 31 33 33 37 35 > 33 37 38 34 33 31 35 30 4 > 36 35 37 36 35 30 37 38 40 > 37 38 39 37 33 31 37 33 34 > 38 40 46 38 40 45 38 40 44 > 38 39 43 38 39 42 38 39 41 > 38 37 35 39 38 40 41 39 43 > 41 39 42 42 39 43 44 40 46 > 44 40 45 45 40 46 > > 104 !NPHI: dihedrals > 4 30 29 31 4 30 29 27 > 4 30 35 36 4 30 35 37 > 4 26 24 25 4 26 24 23 > 4 26 22 20 4 26 22 27 > 5 4 26 24 5 4 26 22 > 5 4 30 29 5 4 30 35 > 6 4 26 24 6 4 26 22 > 6 4 30 29 6 4 30 35 > 7 4 26 24 7 4 26 22 > 7 4 30 29 7 4 30 35 > 8 10 23 18 8 10 23 24 > 8 10 14 15 8 10 14 16 > 8 10 14 17 10 23 18 19 > 10 23 18 20 10 23 24 26 > 10 23 24 25 11 8 10 23 > 11 8 10 14 12 8 10 23 > 12 8 10 14 13 8 10 23 > 13 8 10 14 14 10 23 18 > 14 10 23 24 15 14 10 23 > 16 14 10 23 17 14 10 23 > 18 23 24 26 18 23 24 25 > 18 20 22 27 18 20 22 26 > 19 18 23 24 19 18 20 22 > 19 18 20 21 20 22 27 28 > 20 22 27 29 20 22 26 24 > 20 18 23 24 21 20 22 27 > 21 20 22 26 21 20 18 23 > 22 27 29 30 22 27 29 31 > 22 26 24 25 22 26 24 23 > 22 26 4 30 22 20 18 23 > 24 26 4 30 24 26 22 27 > 26 22 27 28 26 22 27 29 > 26 4 30 29 26 4 30 35 > 27 29 30 35 27 29 31 32 > 27 29 31 33 28 27 29 30 > 28 27 29 31 29 31 33 37 > 29 31 33 34 29 30 35 36 > 29 30 35 37 30 35 37 33 > 30 35 37 38 30 29 31 32 > 30 29 31 33 31 33 37 38 > 31 33 37 35 31 29 30 35 > 32 31 33 37 32 31 33 34 > 33 37 38 39 33 37 38 40 > 33 37 35 36 34 33 37 38 > 34 33 37 35 35 37 38 39 > 35 37 38 40 36 35 37 38 > 37 38 39 41 37 38 39 42 > 37 38 39 43 37 38 40 44 > 37 38 40 45 37 38 40 46 > 39 38 40 44 39 38 40 45 > 39 38 40 46 40 38 39 41 > 40 38 39 42 40 38 39 43 > > 1 !NIMPHI: impropers > 1 8 3 2 > > 0 !NDON: donors > > > 0 !NACC: acceptors > > > 0 !NNB > > 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > > 1 0 !NGRP > 0 0 0 > > > -- > Rudra > JRF; SNBNCBS > http://www.bose.res.in/~rudra > > A bus station is where a bus stops. A train station is where a train > stops. On my desk I have a work station. > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why?See: http://www.gnu.org/philosophy/no-word-attachments.html > > > Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 Download prohibited? No problem. CHAT from any browser, without download. Go to http://in.webmessenger.yahoo.com/
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