Hi,
the downloaded pdb and accompanying top files look fine, at least I did not find any irregularities with the GlcNAc C6-H atoms.
The rupture is observed after we run the simulation on our server.
I went through the output pdf with the ensemble of 20 .pdb and 20 .top.pdb structures and found a small but obviously crucial difference in the atom notations:
In the .rot.pdb files (where everything is fine) the sugar H6 atoms are denoted exactly as in the input files I get from GLYCAM:
ATOM 562 H61 0YB 35 11.271 -2.043 -4.930
ATOM 563 H62 0YB 35 10.654 -1.823 -6.566
while in the .pdb files (ruptured bonds) they are denoted differently:
ATOM 562 1H6 0YB 35 13.997 1.017 -3.051
ATOM 563 2H6 0YB 35 15.270 2.163 -2.600
I changed the (obviously wrong?) denotations 1H6 and 2H6 against H61 and H62, respectively, and adjusted the number of spaces as present in the .rot.pdb files.
When I open this modified file with PyMOL everything is fine, no ruptured bonds and the sugar connectivity/geometry/bond lengths are as they should be.
Do you have an idea where I have to look in order to remove this mistake made somewhen in the cleanup process? Of course we could also just exchange the lines in all .pdb output files as I did for the file described above, but I am not sure whether this is a proper and "scientific" procedure :)
Thank you
Sebastian Enck
>------------------------------
>
>Message: 36
>Date: Tue, 14 Feb 2012 13:25:59 -0500
>From: "Lachele Foley (Lists)" <lf.list.gmail.com>
>Subject: Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CAK2a3ZET_Zh8Da8ZmAorFbYkwavtYSz9N0PkT0zq4wQNg-YkOA.mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>Are you talking about pdb structures downloaded from our website, or
>the output of a simulation or something else? Have you loaded
>corresponding topology and restart/trajectory files? PDB displays
>often "bond by distance." It's important to know what the topology
>thinks is bonded. If you've loaded the top/crd, how did they look?
>
>
>On Tue, Feb 14, 2012 at 12:09 PM, Sebastian Enck <encks.scripps.edu> wrote:
>> Hello everyone,
>>
>> we are performing calculations with AMBER8 on short glycoproteins (34 residues) containing a GlcNAc linked to Asn.
>> We have built this Asn(GlcNAc) using GLYCAM and the formatting tools provided on the http://glycam.ccrc.uga.edu website, and everything works very nice.
>>
>> Our observation, however, is that in the 20 .pdb output structures the two carbon-proton bonds at the C6 of GlcNAc are broken. One of the two protons always ends up nonbonded, approx. 4-6 angstroms away from the sugar, while the other >proton always gets bonded to a residue neighboring the Asn(GlcNAc) (for example, the adjacent Phe amide becomes - CO-NH2 - ).
>> In the other 20 output structures (.rot.pdb), however, everything is fine.
>>
>> If we run the cleanup script after the calculations, this error is indicated as RMS deviations for the ensemble (GlcNAc is named 0YB, and has residue number 34):
>>
>> ?**** Error in coords for atom: ?1H6- 0Y- ? ?34
>> ?**** Error in coords for atom: ?2H6- 0Y- ? ?34
>> (this message appears once for every .pdf created)
>>
>> We do not know whether this is a common problem when the program tries to handle glycosylated residues, and maybe this problem has been observed before?
>>
>> Thank you for your suggestions,
>> Sebastian Enck
>>
>> __________________________
>> Sebastian Enck, Ph.D.
>> The Scripps Research Institute
>> Beckman Center
>> 10550 North Torrey Pines Road
>> La Jolla, CA 92037
>> encks.scripps.edu
>> _______________________________________________
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 14 2012 - 17:30:02 PST
