VMD-L Mailing List
From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Wed Sep 24 2008 - 23:11:04 CDT
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yes...i tried that but when i with that pdb& psf file i am trying to solvate the molecule with command:
(ao) 1 % package require solvate
1.2
>Main< (ao) 2 % solvate aoq.psf aoq.pdb -t 10 -o aoq_wb
its giving error:
reading structure from psf file aoq.psf
error reading atoms
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>Main< (ao) 3 %
ofcourse the atom with -1 occupency has removed here.
so what should i do to solvate the molecule?
-- 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: Peter Freddolino <petefred_at_ks.uiuc.edu> To: Rudra Banerjee <bnrj.rudra_at_yahoo.com> Cc: vmd-l_at_ks.uiuc.edu Sent: Thursday, 25 September, 2008 9:31:48 AM Subject: Re: vmd-l: psf file generation: once again The solution was suggested by Christopher Chang yesterday: turn off automatic patching. segment U { pdb blah.pdb first none last none } (or, don't just insert your residue into the charmm22 files, which have default patches defined). Peter Rudra Banerjee wrote: > dear friends, > I want to repeat one of my unsolved problem. i have a non std. molecule with initial (before generating psf) pdb file is: > > > #CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 > ATOM 1 CD1 MAC A 1 -3.039 1.934 -0.283 1.00 0.00 C > ATOM 2 CG MAC A 1 -3.189 0.892 0.625 1.00 0.00 C > ATOM 3 CD2 MAC A 1 -2.112 0.042 0.894 1.00 0.00 C > ATOM 4 CE2 MAC A 1 -0.879 0.204 0.276 1.00 0.00 C > ATOM 5 CZ MAC A 1 -0.733 1.261 -0.643 1.00 0.00 C > ATOM 6 CE1 MAC A 1 -1.812 2.120 -0.917 1.00 0.00 C > ATOM 8 C3 MAC A 1 1.315 -0..482 -0.029 1.00 0.00 C > ATOM 9 C2 MAC A 1 1.562 0.544 -0.962 1..00 0.00 C > ATOM 10 C1 MAC A 1 0.512 1.419 -1.262 1.00 0.00 C > ATOM 11 C7 MAC A 1 2.353 -1.354 0.273 1.00 0.00 C > ATOM 12 C6 MAC A 1 3.613 -1.234 -0.321 1.00 0.00 C > ATOM 13 C5 MAC A 1 3.854 -0.212 -1.232 1.00 0.00 C > ATOM 14 C4 MAC A 1 2.827 0.670 -1.563 1.00 0.00 C > ATOM 24 C8 MAC A 1 5.628 -2.116 -0.419 1.00 0.00 C > ATOM 25 CA MAC A 1 -5.107 1.352 1.005 1.00 0.00 C > ATOM 26 CB MAC A 1 -4.392 -0.073 1.897 1.00 0..00 C > ATOM 36 C9 MAC A 1 4.407 -3.273 0.925 1..00 0.00 C > ATOM 7 N MAC A 1 0.123 -0.642 0..571 1.00 0.00 N > ATOM 15 N1 MAC A 1 4.671 -2..189 0.006 1.00 0.00 N > ATOM 16 N2 MAC A 1 -4..299 0.713 1.207 1.00 0.00 N > ATOM 17 HD1 MAC A 1 -3.879 2.612 -0.492 1.00 0.00 H > ATOM 18 HD2 MAC A 1 -2.248 -0.784 1.607 1.00 0.00 H > ATOM 19 HE1 MAC A 1 -1.685 2.949 -1.629 1.00 0.00 H > ATOM 20 H1 MAC A 1 0.669 2.239 -1.978 1.00 0.00 H > ATOM 21 H7 MAC A 1 2.175 -2.167 0.992 1.00 0.00 H > ATOM 22 H5 MAC A 1 4.846 -0.106 -1.696 1.00 0.00 H > ATOM 23 H4 MAC A 1 3.013 1.474 -2.290 1.00 0.00 H > ATOM 27 H81 MAC A 1 6.081 -1.136 -0.148 1.00 0.00 H > ATOM 28 H82 MAC A 1 5.550 -2.185 -1.527 1.00 0.00 H > ATOM 29 H83 MAC A 1 6.270 -2.939 -0.032 1.00 0.00 H > ATOM 30 HA2 MAC A 1 -4.830 2.397 1.270 1.00 0.00 H > ATOM 31 HA1 MAC A 1 -5.986 1..045 1.614 1.00 0.00 H > ATOM 32 HA3 MAC A 1 -5.354 1.307 -0.080 1.00 0.00 H > ATOM 33 HB2 MAC A 1 -5.425 -0.085 2.310 1.00 0.00 H > ATOM 34 HB3 MAC A 1 -4.187 -1.041 1.386 1.00 0.00 H > ATOM 35 HB1 MAC A 1 -3.663 0.071 2.725 1.00 0.00 H > ATOM 37 H93 MAC A 1 3.586 -3.909 0.524 1.00 0.00 H > ATOM 38 H92 MAC A 1 5.323 -3.895 1.040 1.00 0.00 H > ATOM 39 H91 MAC A 1 4.096 -2.858 1.910 1.00 0.00 H > END > > and for this molecule, i have generated my topology file(inserted to charmm22 protein topology file)is: > !MY RESIDUE > > RESI MAC 0.00 > GROUP > ATOM N2 NH2 -0.47 ! > ATOM HA1 HB 0.31 ! > ATOM CA CA 0.07 ! > ATOM HA2 HB 0.09 ! > ATOM HA3 HB 0.00 ! > GROUP ! > ATOM CB CA -0.18 ! > ATOM HB1 HB 0.09 ! > ATOM HB2 HB 0...09 ! > ATOM HB3 HB 0.00 ! > GROUP ! > ATOM CD1 CA -0.115 ! > ATOM HD1 HP 0.115 ! > GROUP ! > ATOM CE1 CA -0.115 ! > ATOM HE1 HP 0.115 ! HE1 H1 H4 > GROUP ! | | | > ATOM CZ CA 0.00 ! HA2 HD1 CE1 C1 C4 H5 H83 > GROUP ! | \ // \ / \\ / \\ / | > ATOM CG CA 0.00 ! HA1-CA CD1 CZ C2 C5 --C8-H82 > GROUP ! | | || | | \ > ATOM CD2 CA -0.115 ! HA3 N2-- CG CE2 C3 C6-N1 H81 > ATOM HD2 HP 0.115 ! | \\ / \ // \ // | > GROUP ! HB1-CB-HB3 CD2 N C7 C9-H93 > ATOM CE2 CA 0.47 ! | | / / \ > ATOM N NR3 -0.47 ! HB2 HD2 H7 H91 H92 > GROUP ! > ATOM C1 CA -0.115 ! > ATOM H1 HP 0.115 ! > GROUP ! > ATOM C2 CA 0.00 ! > ATOM C3 CA 0.00 ! > GROUP ! > ATOM C4 CA -0.115 ! > ATOM H4 HP 0.115 ! > GROUP ! > ATOM C5 CA -0.115 ! > ATOM H5 HP 0.115 ! > GROUP ! > ATOM C7 CA -0.115 ! > ATOM H7 HP 0.115 ! > GROUP ! > ATOM C6 CA 0.07 ! > ATOM N1 NH2 -0.047 ! > ATOM C8 CA 0.08 ! > ATOM C9 CA 0.08 ! > ATOM H81 HB 0.04 ! > ATOM H82 HB 0.04 ! > ATOM H83 HB 0.04 ! > ATOM H91 HB 0.04 ! > ATOM H92 HB 0.04 ! > ATOM H93 HB 0.04 ! > BOND CG CD1 CE1 CZ CZ C1 C2 C3 CE2 CD2 CE2 N C2 C4 C5 C6 N2 CG N1 C6 > BOND N2 CA CA HA1 CA HA2 CA HA3 N2 CB CB HB1 CB HB2 CB HB3 > BOND CD1 HD1 CE1 HE1 C1 H1 C4 H4 C5 H5 C7 H7 CD2 HD2 C7 C3 > BOND N1 C8 N1 C9 C9 H91 C9 H92 C9 H93 C8 H81 C8 H82 C8 H83 > DOUBLE CD1 CE1 CG CD2 CZ CE2 C1 C2 C3 N C4 C5 C6 C7 > > > but when i am trying to generate psf file using vmd using the .pgn file (cku.pgn) > > package require psfgen > topology my-top.inp > #pdbalias residue HIS HSE > #pdbalias atom ILE CD1 CD > segment U {pdb ao_tst.pdb} > coordpdb ao_tst.pdb U > guesscoord > writepdb aoq.pdb > writepsf aoq.psf > > using the command: > $vmd -dispdev text -e cku.pgn > > then i am getting a few extra atom(6 actually) in (0 0 0) position with occupency -1. here is that (part of) generated pdb file: > > 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 > ... > ... > > those occupency with -1 is troublesome and i need to remove them. any idea where i am going wrong?looking fwd for your suggestions. > **NB. plz ignore if there is any double decimal...its somehow due to formatting** > > Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
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