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: Mon Feb 03 2020 - 10:07:57 CST

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

  

-- 
Santanu Santra
Research Scholar 
Molecular Simulation Laboratory
Department of Chemistry
NIT ROURKELA
ROURKELA, 769008

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