[AMBER] Fwd: Bad atom type: C0

From: Manikanthan Bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Fri, 4 Apr 2014 11:27:43 -0400

Dear All,

I am trying to calculate per-residue decomposition analysis using mmpbsa.py
script of amber12. The membrane protein + ligand system consists of Ca+2,
Cl-, and Br- ions. 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
            else if (atype == "Br") then
               x(L165-1+i) == 1.82d0 + 1.4d0
            else if (atype == "Cl") then
               x(L165-1+i) == 1.67d0 + 1.4d0
            else

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

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 - 09:00:03 PDT
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