VMD-L Mailing List

From: Yixin Chen (yixin.chen1_at_ucdconnect.ie)
Date: Tue Mar 12 2024 - 10:30:55 CDT

Hi Cindy, Josh,

Thank you so much for your guidance and advice! I solved the problem.
Two points should be paid attention to. The first one is to have the
correct PSF file. The Candy method is helpful for checking the PSF file,
the topology is important. The second is to use the Mergemols command to
combine two PDB and PSF files, as Josh suggested.
I hope my experience can help more beginners, and thanks again for your
help!

Best regards,
Yixin

On Tue, 12 Mar 2024 at 01:03, Cindy Cregier <cindy.cregier_at_yahoo.com> wrote:

> Hi Yixin,
>
> I'm fairly new to NAMD, but your problem sounds similar to an issue I
> recently had. I see that you're using parameters created from different
> time frames. You'll find that the older parameter file has different atom
> definitions than the newer parameter file. Atoms can be given one name in
> one parameter file and another name in the other parameter file. Sometimes
> even numerical values given in the parameter files change between one
> generation and the next! Also, look at the date of generation. I found
> one file that had the same name, but a different generation date. The
> contents had changed, but they kept the name of the topology file the
> same!
>
> Here's what I did. I made sure that I used only the latest version of
> each topology and parameter file that's out there. I also made sure that
> the topology files used to create my psf and pdb files had the same
> definitions as the parameter files that I used for analysis. Knowing what
> version of a topology file was used in the creation of your pdb and psf
> files helps a lot.
>
>
> I recommend opening the parameter files to see what's in them. Then, open
> your pdb and psf files that you've made. The definitions in your pdb and
> psf files should help you determine what topology files were used to create
> them and therefore what parameter files you need to be using so that all of
> your atoms are defined. Good luck!
>
> On Thursday, March 7, 2024 at 03:27:19 PM EST, Josh Vermaas <
> vermaasj_at_msu.edu> wrote:
>
>
> 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")--00000000000068085606137853b2--