Re: query about the cross term in psf

From: Kshatresh Dutta Dubey (kshatresh_at_gmail.com)
Date: Sat Dec 06 2014 - 14:12:31 CST

Oh sorry Josh, perhaps I pasted wrong error sentence, initially it was
dihedral terms but I added those from previous lipid paramters and
rectified in parameter file. But after that when I re-ran the job it was
giving error:
FATAL ERROR: UNABLE TO FIND CROSSTERM PARAMETERS FOR C NH1 CT1 C NH1
 CT1 C NR3.
Therefore please suggest me about the cross-term.
Thanks

On Sat, Dec 6, 2014 at 9:49 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Cross terms or dihedrals? The error is quite clear. You gave NAMD a psf
> that had a dihedral (*not* a crossterm) term it did not recognize, and to
> prevent you from doing something you didn't intend, it terminated for you
> to avoid wasting computer time. Where did that term come from? Grepping
> around in the charmm topology files, NR3 only shows up in proteins, and HCL
> is an atomtype seen in lipids. Deleting terms wholesale from a psf is a
> downright *dangerous* thing to do, as you will no longer be simulating with
> a force field that has in any way been validated. Is there something
> special about the system that needed a linkage between proteins and lipids?
> If not, do you have any idea how that dihedral term got into your psf?
> -Josh Vermaas
>
>
> On 12/06/2014 01:31 PM, Kshatresh Dutta Dubey wrote:
>
> Dear Users,
>
> I prepared the psf and corresponding pdb using vmd, but it gave error :
> UNABLE TO FIND DIHEDRAL PARAMETERS FOR O C NR3 HCL (ATOMS 7422 7421 7427
> 7448)
>
> I googled the error and found somewhere that deleting the cross-terms in
> psf can make job to run. I did and job is running now. However, I am
> curious to know whether to delete cross-terms in psf is correct or not.
> Please suggest me.
> Thanks in advance.
>
> --
> With best regards
>
> ************************************************************************************************
> Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> Lise Meitner Center for Computational Quantum Chemistry
> Hebrew University of Jerusalem Israel
> Jerusalem, Israel
>
>
>
>

-- 
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:23:06 CST