Hello,
I have simulated a complex containing chains and two lignads pdb ID
:4E1M.pdb . Topology files were created like this
*tleap-1.in*
source leaprc.ff99SB
source leaprc.gaff
BC1 = loadmol2 BI-C-1-new.mol2
BC2 = loadmol2 BI-C-2-new.mol2
loadamberparams BI-C-1-new.frcmod
loadamberparams BI-C-2-new.frcmod
check BC1
check BC2
saveoff BC1 BI-C-1-new.lib
saveoff BC2 BI-C-2-new.lib
quit
*tleap-2.in*
source leaprc.ff99SB
source leaprc.gaff
loadamberparams BI-C-1-new.frcmod
loadamberparams BI-C-2-new.frcmod
set default PBRadii mbondi2
loadoff BI-C-1-new.lib
loadoff BI-C-2-new.lib
complex=loadpdb indimer_complex.pdb
receptor=loadpdb indimer_receptor.pdb
BC1=loadmol2 BI-C-1-new.mol2
BC2=loadmol2 BI-C-2-new.mol2
saveamberparm complex complex.prmtop complex.inpcrd
saveamberparm receptor receptor.prmtop receptor.inpcrd
saveamberparm BC1 BC1.prmtop BC1.inpcrd
saveamberparm BC2 BC2.prmtop BC2.inpcrd
solvatebox complex TIP3PBOX 10.0
charge complex
addions complex Na+ 0
charge complex
addions complex Cl- 0
saveamberparm complex solvated_complex.prmtop solvated_complex.inpcrd
savepdb complex solvated_complex.pdb
quit
After md simulations, I wish to calculate binding energies -
I used this command
MMPBSA.py -O -i mmpbsa.in -o FINAL_MMPBSA_BI_C2.dat -sp
solvated_complex.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
BC2.prmtop -y prod*.mdcrd
where mmpbsa.in is
-------------------------------------------------------------------------------------------------------------------------------------
Input file for running PB and GB
&general
endframe=300, keep_files=2,
receptor_mask=:1-152-304, ligand_mask=:306
/
&gb
igb=5, saltcon=0.100,
gbsa=1,
/
&pb
istrng=0.100,
/
--------------------------------------------------------------------------------------------------------------------------------------------
one ligand is residue 305 in solvated_complex.pdb and other 306
I am getting followeing error -
Error: Sander output is missing values!
VDWAALS = ************* EEL = -10879.9496 EGB = -7164.4331
I had to specify the receptor and ligand mask because there was no best
guess for receptor and ligand mask.\
Could you please help me understand what is wrong.
Thank you
k
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Received on Mon Jul 02 2012 - 01:30:02 PDT
