AMBER Archive (2008)

Subject: AMBER: Error in creating topology file

From: musa özboyacı (
Date: Mon Oct 20 2008 - 06:00:48 CDT

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!

For atom: .R<FEA 502>.A<FE 1> Could not find type: FE
Parameter file was not saved.

*Lib file:*
!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
!entry.FEA.unit.childsequence single int
!entry.FEA.unit.connect array int
!entry.FEA.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
! 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
!entry.FEA.unit.solventcap array dbl
!entry.FEA.unit.velocities table dbl x dbl y dbl z
 0.0 0.0 0.0

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