Dear Amber Users,
I am trying to do a constant pH simulation on a protein-ligand complex with
Amber11 , where the ligand is a sugar ( GlcNAc )6 . I generated the topology
file with the following command
sleap -f leap.in
and the commands in the leap.in file are:
source leaprc.GLYCAM_06
source leaprc.constph
set default PBRadii mbondi2
complex = loadpdb HEL_GlcNAc6_HC2_301-500ps_ave.pdb
saveAmberParm complex prmtop prmcrd
quit
and I got the following output :
Warning: there is an atom HE2 in residue GL442 which does not exist in the
model GL4! This atom will not be created.
Then I did energy minimization with the following parameters:
Run minimization
# 5000 steps of minimization, generalized Born solvent model
&cntrl
imin=1, ntmin=1, maxcyc=5000, ncyc=2500,
cut=30.0, igb=2, saltcon=0.1
ntx=1, irest=0, ntb=0, ntpr=5
ntc=1, ntf=1,
ntwx=10, ntwv=10, ntwe=10, ntwr=10
/
After minimizing the system, I tried to create a cpin file with the
following command :
/amber11/AmberTools/bin/ambpdb -p prmtop < restrt |
/amber11/AmberTools/bin/cpinutil -notresname TYR,LYS > cpin
and got the following error:
| New format PARM file being parsed.
| Version = 1.000 Date = 05/22/06 Time = 12:10:21
Warning: igb value not specified. igb = 5 used as default. Be sure to use
this value for your constant pH simulations!
Error: mbondi2 radius set should be used for constant pH simulations. All
reference energies were calculated using these radii! Set --ignore-warnings
to ignore this warning.
I dont know why this error is coming because I have already set default
PBRadii mbondi2 in the leap.in file and the ibg value to 2 during the energy
minimization. I tried the minimization with igb=5 but again got the same
error while creating the cpin file
Any suggestions please? Thanks in advance
Regards,
Pankhuri
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Received on Wed May 04 2011 - 23:00:02 PDT
