Re: [AMBER] Question about running with a mask to exclude certain residues

From: Supriyo Bhattacharya <>
Date: Fri, 23 Aug 2019 18:07:03 +0000 (UTC)

 Hi,You still need to specify the strip masks in your command using -s and -m (or -n). Just specifying them in the input file is not enough. 
Also, when creating the complex topology by striping residues from the solvated complex, the residues are probably going to be renumbered. So, you may need to account for that when specifying the ligand residue number in the masks. For example, the ligand residue number may not remain 208, since you removed 12 residues in the middle, ligand residue number now becomes 208-12 = 196. Do please verify this, since I am speculating.

    On Friday, August 16, 2019, 5:05:43 PM PDT, A K <> wrote:
 I ran pmemd with a protein-ligand complex, but my prepared pdb still had a few residues missing in the middle of one of its two chains, so there's an unattached part of my protein that's moving around a lot when I view it in VMD and also affecting the backbone RMSD graphs I created with cpptraj. So, I'm trying to re-calculate the free binding energy since I think these unattached residues would probably be affecting the overall free binding energy calculation as well, and might make the default masks not accurate? My protein has three separated parts: residues 1 to 39 are chain A, residues 40 to 51 are chain B, and residues 52 to 207 are also chain B. There's around 6 missing residues between residues 51 and 52 in chain B that are not in my prepared complex, so residues 40 to 51 are moving around a lot when I view the VMD trajectory. My ligands are residue 208. How would I run to exclude residues 40 to 51? I'm not sure why the mask I tried isn't working.

The error I got is this:
Loading and checking parameter files for compatibility...
  File "/amber14/bin/", line 94, in <module>
  File "/amber14/bin/MMPBSA_mods/", line 608, in loadcheck_prmtops
    self.normal_system.Map(INPUT['receptor_mask'], INPUT['ligand_mask'])
  File "/amber14/bin/MMPBSA_mods/", line 130, in Map
    "every atom in the complex topology!")
PrmtopError: provided receptor/ligand masks don't select every atom in the complex topology!
Exiting. All files have been retained.
tar: _MMPBSA*: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
rm: cannot remove `_MMPBSA*': No such file or directory
Job complete

My input file,, is below:
  igb=${i}, saltcon=0.100

The command I used is " -O -i -o complex1_output.dat -sp complex1solvated.prmtop -cp complex1.prmtop -rp receptor.prmtop -lp ligand1.prmtop -eo complex1_output.csv -y prod1_*.mdcrd"

Would I need to recreate the prmtop files again to exclude the residues as well to run or is specifying the masks enough but my syntax is just wrong? Also, the new prmtop files excluding residues 40 to 51 could be created either through leap or, right? Would recreating the prmtops lead to an incompatibility with the coordinate/trajectory files though? Since my mdcrd files had these residues included when I ran the MD. I just want to make sure that my estimated binding energies would still be valid.


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Received on Fri Aug 23 2019 - 11:30:01 PDT
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