VMD-L Mailing List

From: Chia-Ju Hsieh (chiahs_at_mail.med.upenn.edu)
Date: Fri Sep 16 2016 - 15:03:43 CDT

Hi Josh,

Thanks for helping. You are right, those are not errors.
I figure out that the "error" comes out with the incorrect coding format of one of the parameter files when I enable lines of azide in the original parameter file.

Thanks,

Chia-Ju

----- Original Message -----
From: "Joshua Vermaas" <Joshua.Vermaas_at_nrel.gov>
To: "Chia-Ju Hsieh" <chiahs_at_mail.med.upenn.edu>, vmd-l_at_ks.uiuc.edu
Sent: Thursday, September 15, 2016 12:23:17 PM
Subject: Re: vmd-l: Error of NAMD simulation when the structure including azide

Hi Chiaju,

The error comes from there not being a newline at the end of the file.
NAMD expects the last line to be blank, or otherwise will bail out. The
warnings come from duplicate parameter entries that aren't the same. Its
been a while, so I've forgotten how it handles this, but I think the
*second* set of parameters it reads in is the one NAMD uses when
computing bonded terms. These aren't errors, but I'd recommend being
damn sure you are using the parameters you think you are using.

-Josh

On 09/15/2016 10:06 AM, Chia-Ju Hsieh wrote:
> Hi,
>
> I have a small molecular structure conformed as R-N3, and used CgenFF to parametrize the ligand. When I running NAMD simulation seems like it stop at somewhere regarding azide. The error information from the output file are shown in the end of the message.
>
> Is this something wrong with the parameter and topology file?
>
> Thanks,
>
> Chiaju
>
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Warning: DUPLICATE BOND ENTRY FOR NG1D1-NG1D1
> PREVIOUS VALUES k=1244.39 x0=1.1395
> USING VALUES k=696.682 x0=1.2367
> Warning: DUPLICATE ANGLE ENTRY FOR CG2R61-CG2R61-NG1D1
> PREVIOUS VALUES k=42.252 theta0=116.2 k_ub=0 r_ub=0
> USING VALUES k=43.173 theta0=123.94 k_ub=0 r_ub=0
> Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
> k=0.3794 n=2 delta=180
> Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
> k=0.3824 n=2 delta=180
> Warning: DUPLICATE DIHEDRAL ENTRY FOR CG2R61-CG2R61-CG2R61-NG1D1
> PREVIOUS VALUES MULTIPLICITY: 1
> k=0.6104 n=2 delta=180
> Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
> k=0.6519 n=2 delta=180
> Warning: DUPLICATE DIHEDRAL ENTRY FOR HGR61-CG2R61-CG2R61-NG1D1
> PREVIOUS VALUES MULTIPLICITY: 1
> k=0.6397 n=2 delta=180
> Warning: IDENTICAL PERIODICITY! REPLACING OLD VALUES BY:
> k=0.6624 n=2 delta=180
> FATAL ERROR: ABNORMAL EOF FOUND - buffer=*END*
>
>
>