What type of calculation are you trying to run?
My suggestion is to set inp=1, as has been discussed in previous threads on
the mailing list.
Good luck,
Jason
On Sat, Oct 20, 2012 at 8:12 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Oct 20 2012 - 20:00:03 PDT
