I've searched through your database and
found many helpful suggestions, but I am not sure why mdrun successfully
runs on some files but not others. The
protein files are pretty but I get the following results when running
mdrun. (Yesterday I tried attaching the files but they made the email too
big and it got returned)
ABPa1OUT.pdb fails (Number of grid cells is
zero. Probably the system and box collapsed.)
QBPq1OUT.pdb succeeds with errors (some bonds rotated more than 30
degrees)
GBPg1OUT.pdb succeeds
Also, the topology files for ABP and
GBP are made using 1 file, while the QBP topology file is made using 2
files. (when 2 files are used, I edit the topol.top file to have the
posre_A.itp and posre_B.itp files -- #include
"posre_A.itp")
Here are the commands I'm running:
pdb2gmx -f file_name.pdb -o -p <
input.txt
editconf -bt octahedron -f -o -c -d 0.7
genbox -cp conf.gro -cs -o -p
grompp -f -c out.gro -p -o
mdrun -s -o -c -g -e
editconf -bt octahedron -f -o -c -d 0.7
genbox -cp conf.gro -cs -o -p
grompp -f -c out.gro -p -o
mdrun -s -o -c -g -e
Thank you,
Jennifer
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