Dear all,
I was able to get through most of the tutorial
http://ambermd.org/antechamber/pro4.htm<
http://ambermd.org/antechamber/pro4.html>
without
any problems except for then end. When I created the prepi file, I got this
message:
Info: there is a bond linking a non-head and non-tail residue atom (C1) and
an omitted atom (H3).
You need to specifically add this bond in leap using the command
'bond <atom1> <atom2> [order]'
to link C1 to an atom in another residue (similar to disulfide bonds)!
Info: there is a bond linking a non-head and non-tail residue atom (C1) and
an omitted atom (C3).
You need to specifically add this bond in leap using the command
'bond <atom1> <atom2> [order]'
to link C1 to an atom in another residue (similar to disulfide bonds)!
I am not sure exactly what I should do to correct this ( or if I even need
to ). I basically copied what the tutorial did, naming all the atoms
besides the 3 mainchain atoms as OMIT_NAME. Also, when did a quick check of
the structure in xleap (creating a polypeptide NALA 3FY CALA), I was able
to create a sequence using the new amino acid, but it seems that all the
atoms I listed as OMIT_NAME atoms are not displaying.
Thanks,
Matt
On Sun, Feb 12, 2012 at 11:00 PM, Matthew D Antalek <mantale1.binghamton.edu
> wrote:
> Thanks, I did not know about the RED server before. I will try to go
> through with the given tutorial and also look at the one on the RED server.
>
> Thanks,
> Matt
>
>
> On Sun, Feb 12, 2012 at 10:50 PM, Aron Broom <broomsday.gmail.com> wrote:
>
>> Just as another tidbit of information, the RED server has a tutorial for
>> this kind of thing. The problem you are likely coming across, in which
>> you
>> say it is not recognized as an amino acid, is that it doesn't have connect
>> information. You need to add a connect0 and connect1, probably also a
>> head
>> and tail definition. such that it knows your molecule is not a stand-alone
>> molecule, but intended to be used as a fragment. This information tell
>> LeAP which atoms in your residue are meant to connect to other residues
>> when they are a chain. Again I recommend the RED server and associated
>> tutorial, they have a special option on their server for making
>> non-standard amino aicds.
>>
>> ~Aron
>>
>> On Sun, Feb 12, 2012 at 10:40 PM, Jason Swails <jason.swails.gmail.com
>> >wrote:
>>
>> > What do you mean "recognized as an amino acid"? There are very few
>> > situations in the amber programs that actually make use of that
>> distinction.
>> >
>> > Also, if it's a modified amino acid I don't know that gaff is the best
>> > force field to be using to parametrize it. Does FF10 not have the
>> > appropriate parameters? Has anyone else parametrized that residue yet?
>> > (RED Database is a good place to look, as is the Bryce parameter website
>> > that is easily found googling bryce and amber).
>> >
>> > In any case, you should run some short dynamics on some test systems
>> with
>> > your amino acid residue (maybe sandwiched between a couple alanines or
>> > something) and just make sure that some of the properties you can
>> measure
>> > make physical sense (like phi-psi distributions, etc), just to be sure
>> that
>> > nothing is drastically wrong.
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Candidate
>> > 352-392-4032
>> >
>> > On Feb 12, 2012, at 9:41 PM, Matthew D Antalek <mantale1.binghamton.edu
>> >
>> > wrote:
>> >
>> > > Hi all,
>> > >
>> > >
>> > > I am having a bit of trouble with getting AMBER to recognize the
>> > > topology file for a non standard amino acid residue I have created. I
>> was
>> > > able to create the parameter-topology file (.prmtop) but I do not
>> > > understand how to create some other files so that the system can
>> > recognize
>> > > the residue as an amino acid residue. I have tried to work with this
>> > > tutorial : http://ambermd.org/antechamber/pro4.html but I do not have
>> > > access to gaussian. I was able to generate the parameters for the
>> > molecule
>> > > using GAFF, so if anyone knows how to get the system to register the
>> > > molecule as an amino acid that would be great.
>> > >
>> > > Thanks,
>> > > Matt
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: 3fY_2.ac
Received on Mon Feb 13 2012 - 21:00:02 PST
