Dear experts,
I am in my final stage of a part of my research and I have already ran
simulation without any problem. I also ran PBSA and GBSA calculation
without any issues. Now what I want to do to wrap up this part of research
is to perform alanine mutagenesis for some residues (one at a time) to
compare with experimental data. I followed the ras-raf tutorial and
successfully ran the alanine scanning mutagenesis. But when I try to follow
exact same procedure in my system, I get following errors everytime:
Input file:
&general
startframe=500, endframe=3500, interval=5,
verbose=2, keep_files=2, strip_mask=':WAT,CL',
/
&gb
igb=5, saltcon=0.150,
/
&pb
inp=1, radiopt=0, istrng=0.15, fillratio=4.0
/
&alanine_scanning
/
Loading and checking parameter files for compatibility...
File "/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/MMPBSA.py",
line 102, in <module>
app.loadcheck_prmtops()
File
"/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 586, in loadcheck_prmtops
FILES.mutant_ligand_prmtop)
File
"/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 109, in __init__
self._validate()
File
"/opt/software/Amber/14Tools15--Intel-13.0.1.117/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 876, in _validate
raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom
Exiting. All files have been retained.
I understand that the system is saying that there are some issues with the
atom numbers between the complex and the two individual topology file. But
I don't have any clue on why that would be the case as I created the mutant
file by simply copying the wild type file and rename and then remove
whatever extra atoms that are not neede for alanine. For eg:
This was my original arginine in wild type:
ATOM 1216 N ARG 151 -15.543 -12.141 -17.563 1.00
0.00 N
ATOM 1217 CA ARG 151 -15.003 -13.510 -17.573 1.00
0.00 C
ATOM 1218 CB ARG 151 -13.477 -13.506 -17.656 1.00
0.00 C
ATOM 1219 CG ARG 151 -12.889 -12.963 -18.950 1.00
0.00 C
ATOM 1220 CD ARG 151 -13.274 -13.799 -20.149 1.00
0.00 C
ATOM 1221 NE ARG 151 -12.643 -13.306 -21.370 1.00
0.00 N
ATOM 1222 CZ ARG 151 -11.578 -13.860 -21.945 1.00
0.00 C
ATOM 1223 NH1 ARG 151 -11.024 -14.954 -21.426 1.00
0.00 N
ATOM 1224 NH2 ARG 151 -11.081 -13.325 -23.053 1.00
0.00 N
ATOM 1225 C ARG 151 -15.454 -14.294 -16.324 1.00
0.00 C
ATOM 1226 O ARG 151 -15.854 -15.463 -16.437 1.00
0.00 O
To mutate this Alanine, I deleted atoms as follows:
ATOM 1216 N ALA 151 -15.543 -12.141 -17.563 1.00
0.00 N
ATOM 1217 CA ALA 151 -15.003 -13.510 -17.573 1.00
0.00 C
ATOM 1218 CB ALA 151 -13.477 -13.506 -17.656 1.00
0.00 C
ATOM 1225 C ALA 151 -15.454 -14.294 -16.324 1.00
0.00 C
ATOM 1226 O ALA 151 -15.854 -15.463 -16.437 1.00
0.00 O
*I left the atom number as is (after 1218 I left 1225 as in tutorial). This
is the only thing I changed from original complex pdb to create the mutant
one. I did the same to other individual protein complex as well and I save
it with different name. Am I doing this right?? Is there a different way I
am supposed to do this? *
*The only difference between tutorial and my system I can see is the
numbering of atoms. When ras-raf is separated into ras and raf the
numbering of atoms in the tutorial starts from 1 to whatever for ras.pdb
and again 1 to the end for raf.pdb.In <
http://raf.pdb.In> my case the atom
number is 1 to 464 for first protein and then it starts from 465 for
another individual protein. Does this numbering of atoms matter? This is
the only difference I can find between the tutorial and my system.*
*Weird thing is that I tried to rum PB/GB without alanine scanning part in
the script and I don't get any such error message and the calculation
proceeds without any problem, using the same prmtop files for both wild
type and mutant type. As soon as I add "&alanine_scanning" part at the end
of the script I get the above error message. Isn't this weird? If there is
any problem with prmtop of either the wild type or mutant type why would
the PB and GB proceed without any error even though I am using the same
topology files? *
*I have gone everywhere possible to sort this out (for almost two weeks)
but not any luck. So please somebody help me to figure this out. I can send
the topology files if that helps. I am stuck almost towards the end of this
research. So any help would be deeply appreciated.*
*Thank you,*
*J.S*
*Michigan State University*
*Graduate Student*
*Department of Chemistry*
*East Lansing MI*
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Received on Mon Apr 11 2016 - 19:30:04 PDT
