VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Aug 26 2013 - 12:17:44 CDT

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
>>>
>>>
>>>
>>>
>
>
>
>