I would like to calculate the binding free energy of trypsinogen to BPTI. Trypsinogen contains a Ca2+ ion, which I suspect is the problem with this calculation.
Thanks for your advice, but where do I set the inp=1?
I'll try to find it in previous threads.
Rami
On Oct 20, 2012, at 10:42 PM, Jason Swails wrote:
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<mailto: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<mailto:roman.osman.mssm.edu>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Roman Osman
roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
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Received on Sun Oct 21 2012 - 18:00:04 PDT
