VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue May 28 2013 - 16:27:32 CDT

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
>>
>
>
>
> --
> Jiawei Xu
> 

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