AMBER Archive (2004)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Mar 02 2004 - 11:44:13 CST

Dear Scopio,

In order for you to be able to run classical molecular dynamics simulations
you will need to define parameters for bacteriochlorophyll. I suggest you
check the literature to see if there are any published AMBER parameters for
BCL and use these. You would need to create a new residue called BCL in leap
and then define atom types and charges for all of the atoms.

Alternatively you could try using Antechamber (included with Amber 7). This
should be able to load your pdb and will calculate charges and parameters
for you. Note however that antechamber is really designed for simple organic
molecules. Thus if you use it make sure you are aware of the issues
involved. Check the charges and parameters you get, are they sensible etc...
Be wary of any results you obtain.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |
 

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of scopio
> Sent: 02 March 2004 00:01
> To: amber_at_scripps.edu
> Subject: Re: AMBER: xleap don't recognize my residue/atom
>
> 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-s
h-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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> >
> >
> >
> >
>

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