From: Santanu Santra (santop420_at_gmail.com)
Date: Mon Feb 03 2020 - 22:43:31 CST
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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