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: Tue Feb 04 2020 - 09:02:41 CST

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. Psfgen will be updated on the NAMD side soon.

 

Please add the line “auto angle dihedral” to the segment section of your psfgen script, and “vpbonds 0” after resetpsf command. Please check the manual for more information about these commands (https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf)

 

I hope this helps.

 

Best,

 

João

From: Santanu Santra <santop420_at_gmail.com>
Date: Tuesday, February 4, 2020 at 6:32 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,

 

In addition to my previous email, I have also tried with nightly build version of NAMD, but still the same error is coming. For clarification of the issue, I am attaching the files::

=======================================================================

my psfgen input file code ::

-------------------------------------------------------------

package require psfgen
resetpsf

topology toppar_drude_master_protein_2013f.str

segment INA {
first GNTE
        pdb ins_A.pdb
last CTER
}
coordpdb ins_A.pdb INA

guesscoord
writepdb drude_prot_vac.pdb
writepsf drude_prot_vac.psf

----------------------------------------------------------

==========================================

============================================

 

The psfgen log file ::

------------------------------------------

psfgen_out.log (attached herewith)

-------------------------------------------

 

Any kind of help is highly appreciated.

 

Thanks and Regards

 

Santanu Santra

 

 

 

 

On Tue, Feb 4, 2020 at 10:13 AM Santanu Santra <santop420_at_gmail.com> wrote:

Hi Sir,

          Thanks for the reply. Currently I'm using NAMD 2.12 . In my psf file "auto angles dihedrals" segment is present for protein. Again I have created the structure with vpbonds 0 but same problem is coming during minimization.

 

I have a gentle query::

 

 In ANGLE section "CD2O1A OD2C1A LPDO1" combination is absent. So is it required to put the values for those combinations including lone pairs from any other resources or it will automatically take care of that?

 

Thanks and regards

 

Santanu Santra

 

 

 

On Mon, Feb 3, 2020 at 9:37 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

Before I forget again,

 

Please make sure that you have the line “auto angles dihedrals” when building your protein segment(s).

 

Best,

 

João

 

From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Date: Monday, February 3, 2020 at 9:50 AM
To: <namd-l_at_ks.uiuc.edu>, Santanu Santra <santop420_at_gmail.com>
Subject: Re: namd-l: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1

 

Hi Santanu,

 

A couple of questions:

 
Did you prepare the structure with the option vpbonds 0?
Which version of NAMD are your running? Did you try the nightly build?
 

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: Sunday, February 2, 2020 at 10:24 PM
To: <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1

 

The error is coming for every lone pairs :::

 

Another error log is

==========================

 

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 (ATOMS 8 9 11)

Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 (ATOMS 8 9 11)

Aborted (core dumped)

======================================

thanks for any help

santanu santra

 

 

On Mon, Feb 3, 2020 at 9:30 AM Santanu Santra <santop420_at_gmail.com> wrote:

Hi everyone,

            I tried to model one model protein in drude forcefield (toppar_drude_master_protein_2013f.str) and successfully generated the structure by psfgen. But when I am trying to minimize it in namd, it is showing some error throwing message of "unable to find the angle parameter for lone pairs and two other atoms". I checked the ANGLE section in the *.str file to find the combination of these three atoms but it was not there.

 

Can anyone please suggest me where from I can get the Ktheta and Theta0values for those angles including lone pair as one of these three atoms.

 

Exact error log is ::::

=====================================================

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR LPD OD2C1A LPD (ATOMS 91 87 92)

Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR LPD OD2C1A LPD (ATOMS 91 87 92)

Aborted (core dumped)

==================================================

 

The section of pdb for which it is throwing error is as follows :

================================================

ATOM 8 C GLY 1 -2.504 6.616 3.758 1.00 0.00 XXX C
ATOM 9 O GLY 1 -1.357 7.045 3.786 1.00 0.00 XXX O
ATOM 10 LPOA GLY 1 -0.585 6.409 3.797 0.00 0.00 XXX H
ATOM 11 LPOB GLY 1 -1.192 8.031 3.797 0.00 0.00 XXX H

===========================================================

 

Any kind of suggestion is highly accepted.

 

Thanks and regards

 

Santanu Santra

 

 

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