I am using MMPBSA.py.MPI in amber12.
One molecule contains a Ca+2 atom, which I have defined in a Ca2.lib as C0
(below is the Ca2.lib)
The program stops with the following message:
bad atom type: C0
CalcError: /packages/amber/12n/src/amber12/bin/sander failed with prmtop ./trypgn_bpti_nw.top!
as if the Ca (C0) is not recognized in sander.
I would be grateful for a suggestion what to do.
Rami
Ca2.lib
!!index array str
"Ca2"
!entry.Ca2.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"Ca" "C0" 0 1 17825795 1 20 2.000000
!entry.Ca2.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"Ca" "C0" 0 -1 0.0
!entry.Ca2.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.Ca2.unit.childsequence single int
2
!entry.Ca2.unit.connect array int
0
0
!entry.Ca2.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
!entry.Ca2.unit.name single str
"Ca2"
!entry.Ca2.unit.positions table dbl x dbl y dbl z
1.925926 -1.925926 0.0
!entry.Ca2.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
0 0 0 0 0 0
!entry.Ca2.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"Ca2" 1 2 1 "?" 0
!entry.Ca2.unit.residuesPdbSequenceNumber array int
0
!entry.Ca2.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.Ca2.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
Roman Osman
roman.osman.mssm.edu
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Received on Sat Oct 20 2012 - 17:30:03 PDT
