AMBER Archive (2008)

Subject: Re: AMBER: Error in creating topology file

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Mon Oct 20 2008 - 07:34:40 CDT

Hi,

    Although you have library file prepared. You still need to provide
force field parameter for the Fe ion. If there is no bond between Fe
and other atom, you just need to provide the VDW parameter of Fe,
otherwise you need to provide the bond, angle and dihedral parameters.

    You should write the parameter in amber's frcmod format (there are
plenty of examples under directory amber/dat/leap/parm), and load it
in leap using the command "loadAmberParams".

    Then you can save your topology file.

    Sincerely,

    Wei

On Mon, Oct 20, 2008 at 6:00 AM, musa özboyacı <musaozboyaci_at_gmail.com>wrote:

> Dear all,
> I have a problem in preparing topology and parameters for a system which
> contains a Fe ion. I am pretty sure that I have prepared library file for
> the ion properly and for Zn ion there seems to be no problem. Any help will
> be appreciated. Thanks in advance!
>
> *Error:*
> For atom: .R<FEA 502>.A<FE 1> Could not find type: FE
> Parameter file was not saved.
>
> *Lib file:*
> "FEA"
> !entry.FEA.unit.atoms table str name str type int typex int resx int
> flags int seq int elmnt dbl chg
> "FE" "FE" 0 1 131075 1 26 2.000000
> !entry.FEA.unit.atomspertinfo table str pname str ptype int ptypex int
> pelmnt dbl pchg
> "FE" "FE" 0 -1 0.0
> !entry.FEA.unit.boundbox array dbl
> -1.000000
> 0.0
> 0.0
> 0.0
> 0.0
> !entry.FEA.unit.childsequence single int
> 502
> !entry.FEA.unit.connect array int
> 0
> 0
> !entry.FEA.unit.hierarchy table str abovetype int abovex str belowtype
> int belowx
> "U" 0 "R" 1
> "R" 1 "A" 1
> !entry.FEA.unit.name single str
> ""
> !entry.FEA.unit.positions table dbl x dbl y dbl z
> -29.483000 -21.509000 -20.873000
> !entry.FEA.unit.residueconnect table int c1x int c2x int c3x int c4x
> int c5x int c6x
> 0 0 0 0 0 0
> !entry.FEA.unit.residues table str name int seq int childseq int
> startatomx str restype int imagingx
> "FEA" 501 2 1 "?" 0
> !entry.FEA.unit.residuesPdbSequenceNumber array int
> 1
> !entry.FEA.unit.solventcap array dbl
> -1.000000
> 0.0
> 0.0
> 0.0
> 0.0
> !entry.FEA.unit.velocities table dbl x dbl y dbl z
> 0.0 0.0 0.0
>
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