VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Jun 04 2013 - 11:55:58 CDT

Hi Eddie,

I don't know enough about why it appears to be in autopsf as a special
case to be very helpful, but again, if there isn't a patch declaration
in the topology files you are giving to autopsf, I always was under the
impression that the patching process will fail. So somewhere in your
specific the charmm27 topology file I'd expect to see a:

PRES CYSD (charge)
atom declarations (atom deletions and redefining the charges.

and since this is missing from charmm36, psfgen complains that the patch
is impossible to do and dies. If this patch doesn't exist in your
charmm27 topology file, I have no clue why it works if you include it
but fails if you don't. :(

-Josh

On 6/4/13 2:11 PM, Prof. Eddie wrote:
> Is there some reason the patch no longer works?
> Eddie
>
>
> On Wed, May 29, 2013 at 8:56 AM, Prof. Eddie <eackad_at_siue.edu
> <mailto:eackad_at_siue.edu>> wrote:
>
> Hi Josh,
> I found it on the web
> (https://github.com/thatchristoph/vmd-cvs-github/blob/master/plugins/autopsf/autopsf.tcl thanks
> to
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14406.html)
> as a patch to deprotinate a cystine when you will place a metal
> near it. I did not modify the charmm27 force field to include it
> (beyond what I feel comfortable doing).
>
> Should I just try and find the line in the charmm27 inp file and
> place it in a charmm36 file? How does everyone else deprotinate
> their cystines?
> Thanks,
> Eddie
>
>
> On Wed, May 29, 2013 at 7:52 AM, Josh Vermaas
> <vermaas2_at_illinois.edu <mailto:vermaas2_at_illinois.edu>> wrote:
>
> 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 <tel:%28618%29%20650-2390>
>
>
>
>
> --
> _________________________________________________________
> 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>
>
>
>
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390