Re: Re: alpha character error in the psf file

From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Wed Jan 28 2009 - 07:22:51 CST

Thank you very much!! Yes, it was the error!

-----Original Message-----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
Date: Wed, 28 Jan 2009 07:18:52 -0600
Subject: Re: namd-l: alpha character error in the psf file

Hi Ozge,
how did you generate this psf file? Was it hand-edited at all? The
number of dihedrals declared in the NPHI line is larger than the number
of dihedrals present in the file, so namd continues reading and tries to
read
!NIMPHI: impropers
as a dihedral.

You should make sure the number of bonds/angles/etc. present in the file
match what is declared.
Best,
Peter

OZGE ENGIN wrote:
> Hi All,
>
> While I am trying to create a psf file for my molecule, but I got the following error:
>
> FATAL ERROR: ALPHA CHARCTER ENCOUNTERED WHILE READING DIHEDRALS FROM PSF FILE
>
> I looked at the mailing list and saw that somebody has also encountered with the same error, but his message was not replied. I also looked at the code. I think such an error is the result of having a character rather than having a number in the dihedral section of psf file. However, the psf file looks OK.
>
> I am attaching the psf file. I was stuck with this error.
>
> Thanks in advance ...
>
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University

Ozge Engin
=================================
Computational Science & Engineering
Koc University

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