From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Jun 04 2013 - 07:11:31 CDT

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> 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>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
>

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