Re: force field for replica exchange with NAMD

From: Sndor Kovcs (skovacs_at_wustl.edu)
Date: Thu Oct 28 2010 - 17:47:21 CDT

Greetings,

I had this problem earlier when I tried to run something similar using
the REMD scripts.

Make sure to add one line to your base.namd file after you define your
parameters:

parameters par_all27_prot_lipid_na.inp
paratypecharmm on

Hope this helps!

Sándor

Sándor Á. Kovács
President, Association of Graduate Engineering Students (AGES)
Ph.D. Candidate and Graduate Research Assistant - CAML Lab
Department of Energy, Environmental and Chemical Engineering
Washington University in St. Louis - St. Louis, MO 63130 - U.S.A.

On Oct 28, 2010, at 3:40 PM, 俞翔 wrote:

> Hi Jim,
>
> I tested replica exchange with Charmm27 force field. namd
> immediately shows error like (re.out):
>
> errpipe 8: FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER FILE
> par_all27_prot_lipid.prm
> errpipe 3: Reason: FATAL ERROR: UNKNOWN PARAMETER IN XPLOR PARAMETER
> FILE par_all27_prot_lipid.prm
> errpipe 8: LINE=**>CHARMM22 All-Hydrogen Parameter File for Proteins
> and Lipids <<*
>
> I am sure there is no error in my Charmm27 force field and the
> replica exchange scripts have not been modified. So the error
> showing above should be that Charmm27 force field could not be
> correctly read at the beginning of simulation, but I don't know why.
>
> If I modify the forece field as the example did but without adding
> CMAP, namd will then report error when it can not find CMAP like
> (re2.out):
> errpipe 6: ------------- Processor 0 Exiting: Called CmiAbort
> ------------
> errpipe 6: Reason: FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR
> C NH1 ! CT1 C NH1 CT1 C NH1
>
> This is why I am asking how to put CMAP into the force field for
> replica exchange previously. I checked namd-l and found out that
> some people who used Charmm22 force filed directly also faced the
> similar problem that Charmm22 could not be correctly read but none
> reply was given at that time.
>
> Could I know how force filed is read by namd?
>
> Thank you very much,
>
> Xiang
>
> > Date: Thu, 28 Oct 2010 14:18:46 -0500
> > From: jim_at_ks.uiuc.edu
> > To: yuxiang8057155_at_hotmail.com
> > CC: namd-l_at_ks.uiuc.edu
> > Subject: Re: namd-l: force field for replica exchange with NAMD
> >
> >
> > That is just an (ancient) example simulation. You can do replica
> exchange
> > with any force field. Set up, minimize, and equilibrate your
> system as
> > usual and then incorporate it into the replica exchange scripts.
> >
> > -Jim
> >
> > On Thu, 28 Oct 2010, Xiang! Yu wrote:
> >
> > > Hello all,
> > >
> &g! t; > NAMD gives a replica exchange example. The example uses
> alain.params which is modified from Charmm19 force field. I want to
> do REMD simulation with Charmm27 force field. I generate a force
> field with the parameters of bond, angle, dihe, impr and nonbonded
> directly coming from Charmm27. But I do not know how to put CMAP
> parameters into this modified force field so it can be read correctly.
> > > I try to run REMD simulation with the modified force field which
> misses CMAP part, an error "FATAL ERROR: CAN"T FIND CROSSTERM
> PARAMETERS FOR C NH1 CT1 C NH1" will quickly comes out. So could
> anyone with experience of REMD tell me how to add CMAP into the
> force field for REMD, or how to skip CMAP correction during
> simulation?
> > >
> > > Thank you,
> > >
> > > Xiang
> >
> <re.out><fold_synuclein.conf><synuclein_base.namd><re2.out>

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