Hello!
I am working on a series of analysis using MMPBSA.py (ambertools18) to
measure binding energy between the strands of a collagen system that
involves three peptide chains, each 21 residues long.
To measure the binding energy between strand 1 and strands 2 and 3 I am using:
ante-MMPBSA.py -p col.topo -c c.topo -r r.topo -l l.topo -m :1-21 -s
:WAT,Na+,Cl-,K+
MMPBSA.py -O -i mmpbsa.in -cp col.topo -sp c.topo -rp r.topo -lp
l.topo -y vacuo.nc
The program ends with:
raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom
Exiting. All files have been retained.
If I check the files, I can see that the number of atoms of the
topologies is correct:
$ head r.topo
%VERSION VERSION_STAMP = V0001.000 DATE = 05/15/18 14:36:05
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
255 15 121 147 298 216 624 622 0 0
$ head l.topo
%VERSION VERSION_STAMP = V0001.000 DATE = 05/15/18 14:36:07
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
510 15 242 294 596 432 1248 1244 0 0
$ head c.topo
%VERSION VERSION_STAMP = V0001.000 DATE = 05/15/18 14:36:03
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
765 15 363 441 894 648 1872 1866 0 0
255+510= 765, which matches the topology of the complex...
Trying another strategy to figure out the error, I striped all waters
and ions from the topology and used:
ante-MMPBSA.py -p vacuo.topo -c c.topo -r r.topo -l l.topo -m :1-21
MMPBSA.py -O -i ~/collagen/mmpbsa.in -cp vacuo.topo -sp c.topo -rp
r.topo -lp l.topo -y vacuo.nc
Now the program stops with:
File "~/amber18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 932, in CheckConsistency
(i + 1))
PrmtopError: Inconsistent charge definition for atom 39!
Exiting. All files have been retained.
Atom 39 from the topology is part of a glycine from residue 4:
> printdetails :4
The mask :4 matches 7 atoms:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth
Mass Charge GB Radius GB Screen
39 4 GLY N N 7 1.8240 0.1700
14.0100 -0.4157 1.5500 0.7900
40 4 GLY H H 1 0.6000 0.0157
1.0080 0.2719 1.3000 0.8500
41 4 GLY CA CX 6 1.9080 0.1094
12.0100 -0.0252 1.7000 0.7200
42 4 GLY HA2 H1 1 1.3870 0.0157
1.0080 0.0698 1.3000 0.8500
43 4 GLY HA3 H1 1 1.3870 0.0157
1.0080 0.0698 1.3000 0.8500
44 4 GLY C C 6 1.9080 0.0860
12.0100 0.5973 1.7000 0.7200
45 4 GLY O O 8 1.6612 0.2100
16.0000 -0.5679 1.5000 0.8500
I have tried eliminating the entire strand and doing the same tests
with the remaining strands and the same error happens in the same
atom...
I will continue to try to debug the error, but any insight about what
is wrong is appreciated.
Thank you!
Rodrigo.
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Received on Tue May 15 2018 - 15:00:04 PDT
