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

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Feb 06 2020 - 10:42:41 CST

I am glad that you were able to prepare your structure with Charmm-gui.
 
Just a note on the terminal patches. PSFGEN reads the lines "PATCHING ..." at the end of the residues definition to detect what are the default patches for terminals. If one defines the "first" and "last" in psfgen script, these definitions will overwrite what is in the topologies.
 
In this case, if "NTER" had not been defined as "first," psfgen would have applied the correct N-terminal patch.

Best,

João

On 2/6/20, 10:06 AM, "Santanu Santra" <owner-namd-l_at_ks.uiuc.edu on behalf of santop420_at_gmail.com> wrote:

    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=

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