Dear all,
I'm trying to run ante-MMPBSA to make the topologies for MMPBSA, and for my
system it works fine when I try this on AmberTools14-
ante-MMPBSA.py -p 1T5A_FBP4_DE.prmtop -c 1T5AFBP4_com_SM1.prmtop -r
1T5AFBP4_rec_SM1.prmtop -l 1T5AFBP4_lig_SM1.prmtop -s
':WAT,:Cl-,:1045-2088' -n ':1-522'
However, when I try to run the corresponding command, as my protein is a
tetramer, and I'm trying to look at the dimer interactions with MMPBSA
by splitting it along the dimer interface to give two monomer-monomer
systems in order to save time-
ante-MMPBSA.py -p 1T5A_FBP4_DE.prmtop -c 1T5AFBP4_com_SM2.prmtop -r
1T5AFBP4_rec_SM2.prmtop -l 1T5AFBP4_lig_SM2.prmtop -s ':WAT,:Cl-,:1-1044'
-n ':1045-1566'
It gives me an IndexError-
Stripping :WAT,:Cl-,:1-1044 (solvent) from original topology, output is
1T5AFBP4_com_SM2.prmtop
Done stripping solvent!
Creating receptor topology file by stripping :1045-1566 from
1T5AFBP4_com_SM2.prmtop
Done creating receptor topology file!
Creating ligand topology file by stripping !(:1045-1566) from
1T5AFBP4_com_SM2.prmtop
Error: Creating ligand topology failed!
Loaded Amber topology file 1T5AFBP4_com_SM2.prmtop
Reading input from STDIN...
> Removing mask '!(:1045-1566)' (16206 atoms) from the topology file.
Traceback (most recent call last):
File "/home/lepus/amber14/bin/parmed.py", line 159, in <module>
parmed_commands.cmdloop()
File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
stop = self.onecmd(line)
File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
return func(arg)
File "<string>", line 1, in <lambda>
File "/home/lepus/amber14/bin/ParmedTools/parmed_cmd.py", line 141, in
_normaldo
action.execute()
File "/home/lepus/amber14/bin/ParmedTools/ParmedActions.py", line 1163,
in execute
self.parm.delete_mask(self.mask)
File "/home/lepus/amber14/bin/chemistry/amber/_amberparm.py", line 664,
in delete_mask
self.remake_parm()
File "/home/lepus/amber14/bin/chemistry/amber/_amberparm.py", line 440,
in remake_parm
self._fill_res_container()
File "/home/lepus/amber14/bin/chemistry/amber/_amberparm.py", line 637,
in _fill_res_container
self.parm_data['POINTERS'][NRES]-1]-1,
IndexError: list index out of range
That said, I'm able to work around it by just isolating the portions one at
a time as monomers from the main complex itself, and then repeating with
different ligand masks two more times to create the required files.
I'm curious of what's causing it to fail- I've checked my mask in ambmask
to make sure that I'm selecting all the residues I want, which it seems to
be doing, but the error messages that I'm getting seem to suggest the
problem is in my ligand mask.
Best,
Kenneth
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Mon Feb 02 2015 - 12:00:06 PST
