From: Santanu Santra (santop420_at_gmail.com)
Date: Thu Feb 06 2020 - 00:28:01 CST
Many many thanks for your reply sir.
(1) I have installed alpha version of vmd and in TK console put the
suggested command. In this process I have generated one psf and pdb files
but with two error statement in the console . These are ::
*psfgen) ERROR! Failed to parse autogenerate statement. Line 294:
AUTOGENERATE ANGLES DIHEDRALS PATCH DRUDE !note use of DRUDE and
PATCHpsfgen) ERROR! Failed to parse autogenerate statement. Line 294:
AUTOGENERATE ANGLES DIHEDRALS PATCH DRUDE !note use of DRUDE and PATCH*
*--------------------------------------------------------------------------------------------------------------------------------------*
But it is generating psf and pdb files.
(2) My script for psfgen was :
=================================================================
*package require psfgenresetpsfvpbonds 0topology
toppar_drude_master_protein_2013f.strsegment INA {first NTER pdb
ins_a.pdblast CTERauto angle dihedral}coordpdb ins_a.pdb
INAguesscoordwritepdb drude_prot.pdbwritepsf drude_prot.psf*
*========================================================================*
(3) Last few lines indicating it generated successfully pdb and psf was as
follows :
================================================================
*psfgen) Info: pdb file complete.psfgen) Info: writing psf file
drude_prot.psfpsfgen) total of 558 atomspsfgen) total of 163 drude
particlespsfgen) total of 39 anisotropy entriespsfgen) total of 78 lone
pairspsfgen) total of 317 bondspsfgen) total of 564 anglespsfgen) total of
823 dihedralspsfgen) total of 51 improperspsfgen) total of 0 explicit
exclusionspsfgen) Structure requires EXTended PSF formatpsfgen) total of 19
cross-termspsfgen) Info: psf file complete.*
*====================================================================*
(4) Once I proceed for minimzation in namd it's showing error statement as
follows::
===========================================================
*FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD31C HDA2A (ATOMS 6 9)*
*=======================================================================*
(5) For reproduction of my result I am attaching pdb file::
=========================================
*ins_a.pdb (attached herewith)*
=============================================
*Comment* : Sir, as you suggested by TK console it is generating psf and
pdb files, but *"auto angle dihedral" *is not working properly. If this is
so, kindly guide me to rectify the error in that statement.
Many many thanks in advance sir.
Regards
Santanu Santra
On Wed, Feb 5, 2020 at 8:49 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:
> Dear Santanu,
>
>
>
> Psfgen is distributed in VMD as a TCL package/plugin, which you use from
> within VMD. You don’t execute the psfgen executable.
>
>
>
> Please install VMD, and open VMD, on the main window: Extensions ->
> TkConsole. Navigate to the folder you have your psfgen script and necessary
> files, and execute the following command: “play <my psfgen input file>”
>
>
>
> You can also execute VMD in text mode: “vmd -dispdev text -e <my psfgen
> input file>”.
> https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html
>
>
>
> I hope this helps.
>
>
>
> Best,
>
>
>
> João
>
>
>
> *From: *<owner-namd-l_at_ks.uiuc.edu> on behalf of Santanu Santra <
> santop420_at_gmail.com>
> *Reply-To: *<namd-l_at_ks.uiuc.edu>, Santanu Santra <santop420_at_gmail.com>
> *Date: *Wednesday, February 5, 2020 at 8:42 AM
> *To: *Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Cc: *<namd-l_at_ks.uiuc.edu>
> *Subject: *Re: namd-l: Re: FATAL ERROR in protein minimization by drude
> model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
>
>
>
> Hello sir, thanks for the reply.
>
> But I am stuck to few silly problems.
>
>
>
> I downloaded *vmd-1.9.4a38.src.tar.gz* and *vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz
> . *Once I untar them, either of two contains one plugin folder. Even in
> *vmd-1.9.4a38.src.tar.gz* , one directory is present in the name of *psfgen.
> I could not find any executable in the name of psfgen. *Kindly guide me
> to get the executable of psfgen. Apart from that everything you have
> suggested in the last mail is clear to me and I made the script file ready.
>
>
>
> If possible can you please attach the executable of psfgen.
>
>
>
> Many many thanks in advance for your help sir.
>
>
>
> Regards.
>
> Santanu Santra
>
>
>
>
>
>
>
> On Tue, Feb 4, 2020 at 8:32 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:
>
> Hi Santanu
>
>
>
> The psfgen log had the information the I information that I was about to
> ask.
>
>
>
> To prepare structures using Drude forcefield, you need to use the latest
> version of psfgen (version 2.0) distributed with the alpha version of VMD--000000000000f22e9e059de24a5c--
--000000000000f22e9f059de24a5e--
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