VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed May 29 2013 - 07:52:53 CDT

Hi Eddie,
I'm looking at my stock CHARMM topology files, and I don't see a PRES
CYSD line in any of them. Is it possible that you modified your CHARMM27
topology file to include a patch to deprotonate a cysteine? If so, you'd
just have to make the same modification to the CHARMM36 topology file.
While this should fix your immediate error message and get you a psf,
I'm still not sure where the original CYSD patch came from, which you
should probably figure out before going too far down the rabbit hole.
Good luck!
-Josh Vermaas

On 5/28/13 11:27 PM, Prof. Eddie wrote:
> Hi Jiawei,
> Yes, that was a typo, thanks. When I include all three mentioned rtf
> files it does work. The problem is the CYSD patch does not.
>
> I have checked and the resid number is correct but the patch is what
> seems to cause the problem (unless I include the charmm27 file).
>
> There is a ligand chain that is not recognize, but I delete that chain
> and only use the Segments identified that are protein.
> Any ideas?
> Thanks for help in advance!
> Eddie
>
>
>
> On Tue, May 28, 2013 at 3:45 PM, Jiawei Xu <jix20.forward_at_gmail.com
> <mailto:jix20.forward_at_gmail.com>> wrote:
>
> Hi, Edward,
>
> First, par_all_36_prot.prm is not a topology file but a parameter
> file.
>
> Second, if it is a typo error,
> It seems that your pdb file has some atom/molecule type not
> included in the top_all36_prot.rtf topology file.
>
> Third, par_all27_prot_lipid_na.inp included prot, lipid, and na.
> Thus you can add all top_all36_prot.rtf, top_all36_lipid.rtf, and
> top_all36_na.rtf files to PSF gen.
>
> Good luck,
> Jiawei
>
>
> On Tue, May 28, 2013 at 3:43 PM, Prof. Eddie <eackad_at_siue.edu
> <mailto:eackad_at_siue.edu>> wrote:
>
> Hi all,
> I'm trying to combine a protein with a drug (ligand). I built
> a psf for the drug (by analogy using charm36_cgenff), merged
> the two and ran it in namd2 as a test. The protein had
> orginally been parameterized with autopsf using vmd's
> par_all27_prot_lipid_na.inp
>
> Since my ligand and protein were parameterized by different
> versions of the force field (charmm36 for the ligand and
> charmm27 for the protein) I thought my next step (aside from
> optimization of the ligand using fftk) is to reparameterized
> my protein with charmm36.
>
> Here I run into a few problems using the package from
> Mackerell's website
> (http://mackerell.umaryland.edu/CHARMM_ff_params.html). If I
> load the topology file par_all_36_prot.prm, delete the ligand
> chain autopsf will generate a error message with no useful
> info I can gather when I try to deprotinate a cystine:
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
> while executing
> "patch CYSD P1:97"
> ("eval" body line 1)
> invoked from within
> "eval "patch [lindex $patch 0] [lindex $patch 1]:[lindex
> $patch 2]""
> (procedure "::autopsf::makepatches_gui" line 17)
> invoked from within
> "::autopsf::makepatches_gui"
> invoked from within
> ".autopsf.patches.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.patches.finish"
> (command bound to event)
>
>
> If I include the topology file par_all27_prot_lipid_na.inp
> then it succeeds but I assume this means it just
> parameterized using charmm27 not 36 as I want/need. Is there
> something I am doing incorrectly?
> Thanks,
> Eddie
>
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390 <tel:%28618%29%20650-2390>
>
>
>
>
> --
> Jiawei Xu
>
>
>
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390