AMBER Archive (2004)

Subject: Re: AMBER: xleap don't recognize my residue/atom

From: scopio (scopio_at_163.com)
Date: Tue Mar 02 2004 - 02:00:31 CST

Thank you for your help!

Actually my problem is not like that in the tutorial you recommended. In
that tutrials, there're two problems for leap to read pdb, one is
'duplicated atoms', another is 'unkown residue'. The first problem is
resolved by adding protons using protonate program. The other problem is
resolved by typed in properties of copper.

My problem is that my pdb have 'unkown residue's contain hundred of
atoms, it's not possible to type in properties of these atoms. Another
questoin is that I don't know what the properties of those atms are.

The atoms in my pdb are all heterogen atoms although most of them are C,
N, O which are very ordinary in standard proein. I think there must have
a method to let leap recognize my 'unkown residue' easily and hope you
can give me any suggestion.

Scopio
scopio_at_163.com

Rhonda Torres Wrote

>Hi Scopio,
>
>To help you build a *.lib file, you should look at the plastocyanin
>tutorial:
>
>http://amber.scripps.edu/tutorial/plastocyanin/pcy-tutorial-sh-1.html#sh-1.1
>
>This will get you started. We are in the process of updating this
>tutorial and the new page should be up soon, however, this shows how to
>make a *.lib (or as named in the tutorial for the modified HIS and MET
>residues, *.in). One thing the current page doesn't state is that you
>need to addAtomTypes for your "new" atoms (the new page states this). As
>an example:
>
>addAtomTypes {
> {"SM" "S" "sp3"}
>}
>
>needs to be included in your xleap commands to recognize the SM atom type
>that was created for the modified MET residue (mem.in).
>
>Hope this helps.
>
>Rhonda
>
>
>
>Rhonda A. Torres
>The Scripps Research Institute
>Department of Molecular Biology
>10550 N. Torrey Pines Rd. TPC 15
>La Jolla, CA 92037
>
>email: torres_at_scripps.edu
>phone: (858) 784-9781
>fax: (858) 784-8896
>
>On Sun, 22 Feb 2004, scopio wrote:
>
>
>
>>Hi there:
>>
>>I'm new to amber, I don't know how to do when xleap don't recognize
>>residue/atom in my pdb file.
>>
>>I have a PDB file named bcl.pdb contains many atoms with several
>>residues. When I check pdb with 'check' command after load this pdb, the
>>error message occured and showed xleap couldn't recognize the types of
>>atoms and residues.
>>=======error msg=====
>> > check bcl
>>Checking 'bcl'....
>>FATAL: Atom .R<BCL 601>.A<MG 1> does not have a type.
>>FATAL: Atom .R<BCL 601>.A<CHA 2> does not have a type.
>>FATAL: Atom .R<BCL 601>.A<CHB 3> does not have a type.
>>FATAL: Atom .R<BCL 601>.A<CHC 4> does not have a type.
>>..........................
>>===================
>>
>>I searched many documents and found the problem could be resolved by
>>1). load a *.off/*.lib file at the start up of xleap
>>2). use addpdbatommap command to correct the atom names
>>3). use Unit Editor in xleap to creat a new unit by filling in the atom
>>types etc.
>>
>>But none of these 3 methods could be operated for the lack of
>>information like below
>>1) how to build an off file ?
>>2) what atom/residue name I should map to ?
>>3) what atom types I should fill in ?
>>
>>
>>Looking forward to your suggestion!
>>
>>scopio
>>scopio_at_163.com
>>
>>
>>
>
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  • chemical/x-pdb attachment: bcl.pdb

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