My problem is that AMBER is not handling that ( ff99SB), there is not sugar unit right now,
when I am loading f.ex pep1.pdb to the tleap i am getting:
Checking 'x'....
WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
FATAL: Atom .R<CLYS 12>.A<HC 24> does not have a type.
Warning: Close contact of 0.177387 angstroms between .R<CLYS 12>.A<OXT 23> and .R<CLYS 12>.A<HC 24>
Warning: Close contact of 1.080436 angstroms between .R<CLYS 12>.A<C 21> and .R<CLYS 12>.A<HC 24>
Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 1 Warnings: 3
the sugar I will add later, do you have any idea how to fix that? the atom type should be ok
Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Dienstag, 1. November 2011 12:35
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides
Urszula,
I looked at your 2 oligopeptide structures; for what I saw they are
only oligopeptides (the default Amber force field topology database
should handle these residues); NO sugar is connected within these
peptides. Sorry if I miss something...
I only found a single open valency at the C-term side of the
oligopeptides. Please, simply explain where/how you want to connected
your sugar unit(s)...
The sugar-peptide connection will be done to the backbone? to the side
chain of a particular amino-acid residue?
regards, Francois
> Thank you for your reply, I attached two of my peptides in pdb format file,
> could you please have a look on them. I am reading the tutorial 3
> but i guess that my peptides are more complex.
> Could you suggest me something, how to start with them? Where to put
> the intra-molecular charge constrains in this case?
>
> Thank you in advance
>
> regards, Urszula
>
> ________________________________________
> Von: FyD [fyd.q4md-forcefieldtools.org]
> Gesendet: Montag, 31. Oktober 2011 17:59
> An: AMBER Mailing List
> Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides
>
> Dear Urszula,
>
>> I need to run MD simulations for a protein with a modified
>> glycopeptides inside.
>> I was wondering if someone could give me some ideas how to prepare
>> parameters/libraries for such as peptides.
>
> You could follow approaches developed . q4md-forcefieldtools.org.
> See for instance:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
> &
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#28
>
> You can find examples of glycoconjugates/glycopeptides in R.E.DD.B. as well:
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/
> http://q4md-forcefieldtools.org/REDDB/projects/F-84/
> http://q4md-forcefieldtools.org/REDDB/projects/F-72/
> http://q4md-forcefieldtools.org/REDDB/projects/F-71/
> All these projects are published & the references and PubMed
> Identifier (PMID) are now available within each project.
>
> If you provide a drawing or a structure of your glycopeptide we could
> help more easily...
>
> regards, Francois
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Received on Tue Nov 01 2011 - 06:30:04 PDT
