Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1

From: Santanu Santra (santop420_at_gmail.com)
Date: Thu Feb 06 2020 - 09:50:39 CST

Thanks for your reply sir. The issue is solved. I have generated it from
charmm gui. A heartly acknowledgement for your help sir. Regards

On Thu, Feb 6, 2020, 9:04 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Hi Santanu,
>
>
>
> Let me address the parsing errors emitted by psfgen. Those errors are
> saying that psfgen failed to parse those lines from the topology.
> Nonetheless psfgen is automatically detecting the angles and dihedrals if
> you have the line “auto angles dihedrals”. Please confirm if you have that
> line in the messages printed by psfgen, or in the header of the psf file,
> in the REMARKS sections, This issue will be addressed in the next alpha
> version of psfgen and VMD.
>
>
>
> Now regarding your pdb, I noticed that the first residue is a Glycine
> (GLY) and that you are applying a NTER patch instead of GNTE (Glycine
> N-terminus (formally GLYP) in polypeptide). Is there any specific reason
> for this?
>
>
>
> If not, please try the following psfen script:
>
>
>
>
> ---------------------------------------------------------------------------------------------------
>
> package require psfgen
>
> resetpsf
>
> vpbonds 0
>
> topology toppar_drude_master_protein_2013f.str
>
>
>
> pdbalias atom ILE CD CD1
>
> pdbalias atom ILE HD1 HD11
>
> pdbalias atom ILE HD2 HD12
>
> pdbalias atom ILE HD3 HD13
>
>
>
> segment INA {
>
> first GNTE
>
> pdb ins_a.pdb
>
> last CTER
>
> auto angles dihedrals
>
> }
>
> coordpdb ins_a.pdb INA
>
>
>
>
>
> guesscoord
>
> writepdb drude_prot.pdb
>
> writepsf drude_prot.psf
>
>
>
>
> ---------------------------------------------------------------------------------------------------
>
>
>
> Please note the pdbalias to make the CD, HD1, HD2, and HD3 match the
> topology CD1, HD11, HD12, and HD13, and the first patch GNTE, which is the
> N terminal patch for a GLY.
>
>
>
> Very important. Make sure that you are using the nightly build, multicore
> version of NAMD. Your namd conf file should include the options “drude,
> drudeTEMP, and drudeDamping” (
> https://www.ks.uiuc.edu/Research/namd/2.13/ug/node25.html)
>
>
>
> I hope this helps
>
>
>
> Best,
>
>
>
> João
>
>
>
> *From: *Santanu Santra <santop420_at_gmail.com>
> *Date: *Thursday, February 6, 2020 at 12:31 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
>
>
>
> In addition to my earlier email, please consider *"auto angles
> dihedrals" *for all * "auto angle dihedral".*
>
>
>
> On Thu, Feb 6, 2020 at 11:58 AM Santanu Santra <santop420_at_gmail.com>
> wrote:
>
> 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--000000000000b28cf6059dea4fa8--

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