Are you using sander or pmemd to run the simulation? If so, then how
are you converting the output trajectories to pdb and rot.pdb files?
Are you using ptraj or cpptraj?
The two ways of specifying hydrogens are just two different
conventions. Not all software recognizes both. So, it isn't really
correct or incorrect, just different. I don't know how the two
conventions arose, but they both seem fairly common. Perhaps there is
a historian among us. :-)
PyMol probably just doesn't have those types of hydrogen names within
its internal knowledge of chemicals. So, it doesn't know that it is
ok to draw bonds to them. Once you renamed them, it recognized them,
and drew bonds for you. If they hydrogens still seem to be a normal
distance away from the atoms to which they are bonded, they (most
likely) haven't actually "ruptured" or broken away. It's more likely
that the software you are using doesn't know what to do with them.
There are good reasons to write certain software to be very picky like
that, and depending on the purpose of your software, it might be more
or less picky.
It is perfectly acceptable, if also tedious, to simply rename the
hydrogens to make happy whatever software you are using. You are
correct to be mindful of spacing as pdb files are formatted by
"column" (number of characters along in a line) rather than
whitespace. Depending on how you extract the pdb or .rot.pdb files,
it might be possible to have some software upstream change the names
for you.
On Tue, Feb 14, 2012 at 8:16 PM, Sebastian Enck <encks.scripps.edu> wrote:
> 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
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Feb 14 2012 - 18:00:02 PST
