VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Aug 26 2013 - 15:38:04 CDT

If you load both the psf and the pdb, the bond should be visible in VMD
(and probably chimera too, although I've never used it). In terms of
methylating residues, they aren't in the standard topology files as far
as I'm aware. If you'd like to make your own patch, I'd take a look at a
part of the NAMD tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node22.html)
to see what these patches look like in the topology file. With great
care it should be doable.
-Josh

On 08/26/2013 03:15 PM, rasti wrote:
>
> Dear Josh,
>
> Hi,
>
> sorry, my bad! You have been right. it works perfectly and the new
> bond appears in the psf file. however it is not visible in viewer
> software (chimera, etc). I have got another question if it is not
> bothering you ... is there any patch for making metylated residues? my
> sequence has got two methylated residues (Val, Phe). if there is none,
> how can i make one?
>
> Best,
>
> Behnam
>
> On 2013-08-26 21:47, Josh Vermaas wrote:
>
>> Hi Behnam,
>> I'm not at all familiar with the system in question, and am a bit
>> confused by your statement that you need a link between residues 1
>> and 77 when the protein is 87 residues long (if I'm interpreting you
>> correctly). What I thought you wanted was a peptide bond to close a
>> cyclic peptide, which would be a LINK patch between residues 87 and
>> 1. Do you have a better way of explaining what end result you were
>> expecting?
>> -Josh
>>
>> On 08/25/2013 05:10 PM, rasti wrote:
>>>
>>> Dear Josh,
>>>
>>> Hi,
>>>
>>> Thank you so much for the hint. I have perform it, but there still
>>> is a little problem here:
>>>
>>> Both last and first residues are Val and there should be a
>>> N1-C77 peptide-bond linking them, but instead the N1-C87 bond keeps
>>> forming after using the patch LINK.
>>>
>>> Best,
>>>
>>> Behnam
>>>
>>> On 2013-08-26 02:04, Josh Vermaas wrote:
>>>
>>> Hi Behnam,
>>> The usual peptide-building tools assume a linear peptide, and so
>>> you'll need to manually add the linkage between the first and
>>> last residue. The important differences are around your segment
>>> definition:
>>>
>>> segment U {
>>> pdb peptide.pdb
>>> auto none #You don't want the default protein behavior of adding
>>> a N-terminal and C-terminal patch to the first and last residues
>>> }
>>> patch LINK U:lastresidueid U:1 #This does the patching.
>>> coordpdb peptide.pdb U
>>> regenerate angles dihedrals #Angles and dihedral terms across
>>> the patch aren't specified in the topology file, so have psfgen
>>> regenerate them automatically
>>>
>>> Consult the psfgen userguide for the exact syntax (I'm operating
>>> off memory, and probably got a detail wrong here or there), and
>>> replace the lastresidueid with the actual id. :)
>>>
>>> Good luck!
>>> -Josh
>>>
>>> On 08/25/2013 02:52 PM, rasti wrote:
>>>
>>> Dear VMD/NAMD users,
>>>
>>> iam trying to build psf file for a cyclic peptide and i keep
>>> facing following problem:
>>>
>>> 1) when i use the pdb relates to the cyclic form peptide
>>> (generated by hyperchem), VMD ignores the cyclic structure
>>> and remove the peptide bond bond between the first and the
>>> last residues adding extra O and N instead.
>>>
>>> package require psfgen
>>>
>>> psfcontext reset
>>> topology top_all27_prot_lipid_modified.rtf
>>> pdbalias atom ILE CD1CD
>>> pdbalias residue HIS HSE
>>> segment U {pdb peptide.pdb}
>>> coordpdb peptide.pdb U
>>> guesscoord
>>> writepsf cyclic.psf
>>> writepdb cyclic.pdb
>>>
>>> any help is really appreciated,
>>>
>>> Behnam
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
>
>
>