Re: Setting up membrane protein simulation from existing conformation?

From: Kenno Vanommeslaeghe (
Date: Wed May 07 2014 - 14:44:00 CDT

First question: toppar_water_ions_namd.str ; download from

Second question: I don't know...

On 05/07/2014 03:17 PM, Per Larsson wrote:
> Dear Namd users
> Apologies of this is a very basic question. I am only starting out with name, having much previous Gromacs experience, but I need to test some of the accelerated md protocols available in namd.
> I am having problems generating a complete psf for my system, which contains one protein, a popc bilayer and water molecules, everything properly ordered.
> I can generate the psf for the protein and membrane, but have run into problems when dealing with the solvent. I am using namd 2.9 and the charmm36 forcefield, recently downloaded from the MacKerell website.
> Here is my complete script to psfgen:
> # Use the specified CHARMM27 topology file.
> topology toppar/top_all36_prot.rtf
> # create an alias for TIP3
> pdbalias residue SOL TIP3
> # Build three segments, one for each chain.
> segment solv {
> auto none
> pdb solvent.pdb
> }
> # Load the coordinates for each segment, and use alias for atom names in the input file
> pdbalias atom TIP3 OW OH2
> pdbalias atom TIP3 HW1 H1
> pdbalias atom TIP3 HW2 H2
> coordpdb solvent.pdb solv
> # Write out the psf file
> writepsf solvent.psf
> Running this in namd 2.9 gives the following errors:
> ---- *
> psfgen)
> psfgen) Created by CHARMM version 36 1
> psfgen) aliasing residue SOL to TIP3
> psfgen) building segment SOLV
> psfgen) disabling angle autogeneration
> psfgen) disabling dihedral autogeneration
> psfgen) reading residues from pdb file foo.pdb
> psfgen) unknown residue type TIP3
> <snip>
> psfgen) extracted 31 residues from pdb file
> psfgen) Info: generating structure...psfgen) unknown residue type TIP3
> failed!
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> Now, this sort of makes sense in that indeed there is no TIP3 residue defined in the toppar/top_all36_prot.rtf file, but raises the question where in the c36-files this is defined precisely? I have seen tutorial material that groups the psfgen of protein and solvent together, and in which they use top_all22_prot.rtf, but that does not help me either, unfortunately.
> My other question is that I have seen hints trying to google my way here that there are potentially issues with feeding pdb-files with large (I have > 100000) numbers of water molecules to psfgen. Is this true, and in this case is the only other option to use the solvate program?
> Sorry for the long mail, but hopefully I can move forward with this fairly quickly with some help from others.
> Cheers
> /Per Larsson

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