From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Tue Jan 07 2014 - 08:05:22 CST
Hi Katherine,
I still think this is not a problem of the NAMD version. I am no expert but
I have passed this stage.
Just closely look at what are these atoms the error message relate to. You
get the error message comes because your psf file has made a dihedral for
these four atoms, but NAMD cannot find the designated parameters when the
simulation is running.
I think a good start will be to see what are these atoms in your protein
system. Probably, you should see if there are newer topology and parameter
files that you can use. You can look here :
http://mackerell.umaryland.edu/CHARMM_ff_params.html
RF
On Tue, Jan 7, 2014 at 12:33 AM, Katherine Parra Pulido <kparra_at_mail.usf.edu
> wrote:
> Hello,
>
> I'm trying to run a minimization on a big system, but have had problems
> with force field parameters (toppar_c31b1<http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c31b1.tar.gz>).
> I'm using namd 2.7 since software update does not depend on me it is
> installed in a cluster.
> I've been searching in mailing list with no success about fatal error:
> CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH.
> Evidently this dihedral is not in prm file I'm using, if copying and paste
> from another file is the solution where should I look for this?
> Thank you for your time, and I'm sorry for any grammatical error, English
> is not my native language.
>
> *KP*
>
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