From: Prof. Eddie (eackad_at_siue.edu)
Date: Wed May 29 2013 - 08:56:48 CDT

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> 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>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> 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 <%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
>
>
>

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390