VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Thu Mar 07 2024 - 13:18:13 CST

Hi Yixin,

Keep the list in the loop, so that the universe can learn about how to
do this. If you have a psf/pdb pair for the membrane, and a psf/pdb pair
for the graphene film, and you are happy with both of them, I usually
recommend another topotools feature, the mergemols command.
https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/#TOC-Utility-Functions
 From what I recall, merge structures calls psfgen in the background, so
in my hands it did some dumber stuff when it doesn't recognize something
in the topology file. Topotools mergemols does not, and is basically
like a fancy copy-paste command.

-Josh

On 3/7/24 1:43 PM, Yixin Chen wrote:
> Hi Josh,
>
> Thank you so much for your reply! Following your guidance, I conducted
> tests on the direct simulation of the lipid membrane using the pdb and
> psf files generated by the VMD Membrane Builder tool directly, and it
> works. The problem should be in the step of converting membrane and
> graphene to psf.
> In the previous test, I used the following command in the Tcl console
> to convert PDB to PSF for both graphene film and lipid (POPC) membrane
> and combine the two using the tool(Merge structure) in VMD.
>
> /package require topotools
> topo retypebonds
> topo guessangles
> topo guessdihedrals mol reanalyze 0
> animate write psf name.psf/
>
>
> Today, to get the correct psf, I attempted to use the provided
> command(in NAMD Tutorial, as shown) for generating psf files. While
> the generation was successful for the lipid membrane, I noticed that
> some information was lost in the process, resulting in an unusual
> appearance when viewed in VMD. For the graphene film, the conversion
> process encountered an error. Specifically, the error message
> indicated: "Error! Fail to recognize XXX (including CA, CD, N, NH...
> which are not included in the pdb) and unknown residue type GRA." I
> think that this error may be attributed to an incorrect topology file.
>
> /package require psfgen/
> /topology top_all27_prot_lipid_na.inp/
> /segment U {pdb myfile.pdb}/
> /coordpdb myfile.pdb U/
> /guesscoord/
> /writepdb myfile .pdb/
> /writepsf myfile .psf/
>
>
> Could you please let me know how to correctly convert the pdb to psf
> for lipid membrane and graphene film and what topology file should be
> used. Thank you very much!!
>
> Best regards,
> Yixin
>
>
> On Wed, 6 Mar 2024 at 15:36, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
> Hi Yixin,
>
> How did you build your psf? The lipid atomtypes should be
> something like CTL2 or CTL3 or something if they are in the lipid
> tail, not C12 or C13. Somehow your atomtype field in the psf is
> populated with atomnames instead, which don’t match atomtypes in
> the parameter file that you loaded. If you started from the
> membrane builder tool in VMD, it is possible that you loaded the
> pdb first into VMD, which sets atomtypes by default based on the
> atomname. Then when you did the merger, it is possible that the
> correct atomtypes were not transferred.
>
> -Josh
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Yixin Chen
> <yixin.chen1_at_ucdconnect.ie>
> *Date: *Wednesday, March 6, 2024 at 10:08 AM
> *To: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: looking for help to solve FATAL ERROR：Didn't
> find vdw parameter for atom type C11
>
> Dear all,
>
> I hope this email finds you well. I am looking for help regarding
> an error that occurred when I ran my simulation in NAMD. */FATAL
> ERROR/**/：/**/Didn't find vdw parameter for atom type C11./*
>
> My simulation model comprises a graphene film and a lipid (POPC)
> membrane, both of which were constructed using the Carbon
> Nanostructure and Membrane Builder tools in VMD. I have combined
> these two components into a single PDB and PSF file. However, upon
> running the simulation, the aforementioned error arises. Upon
> reviewing the PDB file, I noticed that C11 (and similarly C12,
> C13, etc.) is part of the lipid membrane structure.
>
> Initially, I thought that I might miss a parameter file, so I
> included all the necessary topology files in the configuration
> file. Despite this, the error persists. the parameter file I used
> is shown:
>
> /parameters  par_all27_prot_lipid_na.inp/
>
> /parameters  par_all22_prot.prm/
>
> /parameters  par_all36_carb.prm/
>
> /parameters  par_all36_cgenff.prm/
>
> /parameters  par_all36_lipid.prm/
>
> /parameters  par_all36_na.prm/
>
> /parameters  par_all36_prot.prm/
>
> /parameters  par_amber2charmm.inp/
>
> Additionally, I attempted to modify the atom designation from C11
> to C in the PDB, PSF, and reference files, but the error message
> persists with a change in atom type (e.g., "Didn't find vdw
> parameter for atom type C12").
>
>
> If anyone has encountered a similar issue or has expertise in
> troubleshooting NAMD simulations, I would greatly appreciate any
> insights or guidance you can provide. Thank you very much for your
> attention and help!
>
> Best regards,
>
> Yixin
> 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io