Hello everyone,
I am new to amber and a bit lost, trying to perform MMGBSA and MMPBSA
calculations.
I modified a DNA-Protein pdb (1RAM) with pdb4amber and then with
LibreOffice I saved into other two pdb, the ligand (DNA) and the
receptor (Protein). Then I used tleap to create the topology (prmtop)
and the coordinates (rst7) files, without any obvious problem.
1) Should I do something differently to create the topologies and coordinates?
Trying to run MMPBSA.py the following error comes up:
CalcError: /mnt/apps/prebuilt/amber/18/bin/sander failed with prmtop
../complex/TOP_cmplx.prmtop!
Exiting. All files have been retained.
and _MMPBSA_complex_gb.mdout.0 informs me that:
| INFO: Old style inpcrd file read
FATAL: NATOM mismatch in coord and topology files
I checked the top topology and coordinates and the number of atoms is
the same in both files.
I noticed that in _MMPBSA_normal_traj_cpptraj.out says that it striped
Stripping atoms in mask
[:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL], and my complex
contains some waters in its protein. I suspect that this is causing
the mismatch.
2) How can I prevent the stripping?
3) Is it ok to erase the waters from my topology and coordinate files?
I did run the following script for the MMGBSA:
$AMBERHOME/bin/MMPBSA.py -O -i mmgbsa.in -o FINAL_RESULTS_MMPBSA.dat
-sp ../TOP_solveted.prmtop -cp ../complex/TOP_cmplx.prmtop -rp
../protein-recepotor/TOP_protein.prmtop -lp
../DNA-ligand/TOP_DNA.prmtop -y ../Trajectorie/*.nc
with mmgbsa.in :
Input file for running PB and GB
&general
netcdf=1, use_sander=1, startframe=350, endframe=450, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
Thank you very much!!
Bests,
Charalampos
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Received on Tue Sep 24 2019 - 10:00:02 PDT
