From: 俞翔 (datouyu_zju_at_hotmail.com)
Date: Thu Oct 28 2010 - 17:56:58 CDT
Hi Sándor,
I add "paratypecharmm on" in my script and it works on.
Thank you,
Xiang
From: Sándor Kovács
Sent: Thursday, October 28, 2010 6:47 PM
To: 俞翔
Cc: jim_at_ks.uiuc.edu ; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: force field for replica exchange with NAMD
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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