Oh, thanks Jason.
On Tue, Feb 7, 2012 at 1:24 PM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Dear Aron,
>
> It is true. I visualized it in Pymol. Thanks for the suggestion.
> I used the ff99SB and gaff to run again MD for my docked complexes. I'd
> have checked it with xleap.
> Just one thing Im wondering, how AMBER turns to "understand" what bond (in
> small molecules) it should make?
>
> Thank you.
>
> Chinsu
>
>
> On Tue, Feb 7, 2012 at 12:18 PM, Aron Broom <broomsday.gmail.com> wrote:
>
>> I'm fairly certain that AMBER ignores any such information in the pdb. If
>> you are making prmtop and inpcrd files from a pdb you need to make sure
>> that the forcefield you are loading has definitions for everything in your
>> pdb, or else load a library that contains the missing information. You
>> can
>> use the edit function in xleap to check your structure and see if the
>> bonds
>> you intend are present.
>>
>> What program are you using to visualize your pdb afterwards? Programs
>> like
>> PyMol will make assumptions about covalent bonds based on distance
>> information. Therefore, if your structure is insufficiently relaxed
>> (atomic clashes) you will see bonds in the wrong places. If you have been
>> using PyMol maybe swap to VMD instead.
>>
>> ~Aron
>>
>> On Mon, Feb 6, 2012 at 11:05 PM, Chinh Su Tran To
>> <chinh.sutranto.gmail.com>wrote:
>>
>> > Dear Amber users,
>> >
>> > Is it correct that AMBER ignores all CONECT information in the pdb
>> input?
>> > What happens if the pdb contains the small molecules?
>> >
>> > It happened to me that when I convert the prmtop and inpcrd files back
>> to
>> > pdb formatted file using "ambpdb", the structure does not look right to
>> me
>> > (containing wrong connection or bonds), then I also converted the
>> > after_minimization_structure, it looked better but still contained wrong
>> > bonds (e.g 5 connections for a C atom), and after all, my
>> > equilibration_structure's totally wrong.
>> >
>> > Could I ask for any help to explain how it could be? Any clue to
>> avoid/fix
>> > it?
>> >
>> > Thank you.
>> >
>> > Chinsu
>> > _______________________________________________
>> > 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
>>
>
>
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Received on Mon Feb 06 2012 - 21:30:04 PST
