Dear All,
I am trying to calculate per-residue decomposition analysis using mmpbsa.py
script of amber12 and ff99SB. The membrane protein + ligand system
consists of Ca+2 ion. Hence, I have added the following lines to
$AMBERHOME/src/sander/mdread.F90 file after line number 2215
else if (atype == 'C0'.or. atype == 'Ca') then
! Ca radius = 1.3264
x(L165-1+i) == 1.33d0 + 1.4d0
Then, I have recompiled amber12. Now, when I am running decomposition
analysis using mmpsa.py, the following error is shown in the
_MMPBSA_gb_decomp_com.mdin as:
File generated by MMPBSA.py
&cntrl
ncyc=0, cut=999.0, nsnb=99999, gbsa=2,
saltcon=0.1, ntb=0, dec_verbose=1,
imin=5, idecomp=1, extdiel=80.0,
igb=5, surften=0.0072,
/
Residues considered as REC
RRES 1 1495
END
Residues considered as LIG
LRES 1496 1496
END
Residues to print
RES 1 1496
END
END
bad atom type: C0
The following is the input file:
GB and per-residue decomposition
&general
endframe=10, verbose=1,
/
&gb
igb=2, saltcon=0.100,
/
&decomp
idecomp=1, print_res="1-1496"
dec_verbose=1,
/
Can anybody tell me how to properly include the parameters for the ions to
perform the decomposition analysis??
Thanks,
mani
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Received on Fri Apr 04 2014 - 09:30:02 PDT
