VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sat Jan 25 2014 - 23:24:34 CST

Hi Zeynab,

This is because in c36 water and ions have been split off into their own separate stream file. You need another line:

parameters toppar_water_ions.str

Cheers,

Tristan

From: zeynab mohamad hoseyni [mailto:zmhoseyni_at_yahoo.com]
Sent: Sunday, 26 January 2014 3:21 PM
To: Tristan Croll
Subject: Re: namd-l: How to solvate a protein using C36 and not C27

Hi Tristan,

Thanks a lot for your answer. In this way I may have something wrong with the conf file syntax. I have to use both par_all36_prot.prm and par_all36_lipid.prm since I have both protein and membrane.
I put them in configuration file like the following:
# Input
paraTypeCharmm on
parameters par_all36_prot.prm
parameters par_all36_lipid.prm

I'm not sure if this is true as I receive the following error as soon as I run the conf file:

FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE par_all36_prot.prm
LINE=*ATOMS*
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE par_all36_prot.prm
LINE=*ATOMS*

Charm++ fatal error:
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE par_all36_prot.prm
LINE=*ATOMS*

[0] Stack Traceback:
  [0:0] _Z8NAMD_diePKc+0x4a [0x8168572]
Aborted

Would be so thankful if you can help me.
All the Best,
Z.


On Sunday, January 26, 2014 5:07 AM, Tristan Croll <tristan.croll_at_qut.edu.au> wrote:
Hi Zeynab,

I’m using c36 as well. As long as you’re happy using the standard TIP3P water you don’t have to do anything – none of the atom names have changed between CHARMM versions. Your simulation will run fine.

Cheers,

Tristan

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of zeynab mohamad hoseyni
Sent: Sunday, 26 January 2014 2:49 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: How to solvate a protein using C36 and not C27


Dear All,

I intend to use charmm36 for simulation of a transmembrane protein which already crossed a lipid bilayer.
I produced the psf file using c36 but as soon as I want to solvate the system I have to use the
solvent plug-in of vmd. I use the Solvate version 1.4 which uses c27 and not c36. Can anyone guide me how
to solvate the protein using C36?

Thanks in advance,
Zeynab