VMD-L Mailing List

From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Tue Aug 02 2011 - 02:12:54 CDT

Hi, 1- you should modify atom type and write suitable name, for example: REMARK   Materials Studio PDB file REMARK   Created:  Mon Jun 20 09:27:35 Afghanistan Standard Time 2011 CRYST1   16.907   16.907   14.757  90.00  90.00 120.00 P1 ATOM      1 C001   MOL     2      13.811   6.188   0.243  1.00  0.00           C    ATOM      2 C002   MOL     2      13.261   7.495   0.243  1.00  0.00           C    ATOM      3 C003   MOL     2      12.887   8.098   1.473  1.00  0.00           C    ATOM      4 C004   MOL     2      13.981   5.499   1.473  1.00  0.00           C    ATOM      5 C005   MOL     2      11.419   9.628   0.243  1.00  0.00           C 2- after you should modify topology and forcefield, like this example: MASS    20 C     12.01100 C ! ATOM C020 CN 0.00 BOND C001 C002 C002 C003 C003 C004 C004 C005 after these you can make a psf file for your pdb. if you want that, you need to hire a personal consultant. we can send you my hourly rates, if you are interested. Hope this helps you Sajad & Zahra >________________________________ >From: safron saif <safron10_at_gmail.com> >To: vmd-l_at_ks.uiuc.edu >Sent: Monday, August 1, 2011 4:52 PM >Subject: vmd-l: about psf file generation > > >Dear vmd users, > >I am using Materials Studio software to get the structure of Carbon Nanotube (defective).I  got pdb file for the structure from Material Studio.I have created .inp file and .pgn file for creating the psf file based on this pdb file.I am generated the .psf file also.The problem is that the generated .psf file contains only one atom or i am not getting the .psf file for all the atoms.I couldn't understand where i went wrong.I am attaching the .pdb , .inp and .pgn file for CNT with this mail.Please check it and suggest me if you have any idea to solve this problem. > > >thanking you, > >safron, > > > > >