Jason,
It turns out it was very probably the numbering issue from applying the
strip mask- when I change the mask to -s ':WAT,:Cl-,:1-1044' -n ':1-522'
to account for the now absent residues, it worked without any problems. I
hadn't realized that parmed.py would do the sequential renumbering of the
residues, and instead just pull them straight out from the prmtop.
Here are the files
<
https://www.dropbox.com/sh/8ndp2330xe14p29/AABX72CaRygN6gZE7QXI3-fHa?dl=0>,
in case you wanted to see if there was anything else going on.
Best,
Kenneth
On Mon, Feb 2, 2015 at 8:16 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Feb 2, 2015 at 2:57 PM, Kenneth Huang <kennethneltharion.gmail.com
> >
> wrote:
>
> > 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
> >
>
> Looks like a bug in ParmEd and/or ante-MMPBSA.py (quite possibly both).
> ante-MMPBSA.py calls parmed.py to perform its topology stripping. I
> *suspect* that what is happening here is some clunky re-indexing is
> happening. Unlike "typical" ante-MMPBSA.py uses, what you are trying to do
> here is remove the *beginning* of a protein in the 'strip' command and then
> define part of the part that comes afterwards as the ligand.
>
> However, Amber atom indices are always sequentially ordered from 1 to N
> (which is an implicit numbering borne out of a lack of any explicit
> numbering). So, if ante-MMPBSA.py first strips the prmtop of the -s mask
> and *then* applies the ligand mask to the result, your ligand mask could
> very easily point to atoms that no longer exist (since the stripped prmtop
> will no longer have the first 1044 residues). (The error message is likely
> caused because the NRES pointer is not appropriately updated after the
> initial stripping.)
>
> Typically, the "strip_mask" always comes at the end, so that any ligand or
> receptor mask would be the same in both the stripped and unstripped prmtop
> files. If you send me your prmtop files (or, rather, a link to them on
> Dropbox or something since they appear to be very large), I will try to
> isolate the problem and see if I can provide more than speculation.
>
>
> > 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.
> >
>
> This is a less satisfying way to do it, but it's definitely a legitimate
> workaround. You can also use parmed.py (or xparmed.py) directly and do
> your topology file stripping that way.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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here could not dream of heaven?
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Received on Tue Feb 03 2015 - 11:00:03 PST
