ambpdb -p complex.prmtop <eq5.rst> eq5.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 10/13/14 Time = 15:39:06
ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0
but when I use this script
pdb.in:
trajin eq5.rst 1 1 1
trajout try1.pdb pdb
cpptraj complex.prmtop pdb.in => I get the pdb file.
Is it because of ioutfm=1, ntxo=2 in my input files?
Thanks,
Hirdesh
**> I am using PMEMD in AMBER 14 to simulate my protein ligand complex.
After
> > equilibration, I am trying to generate the pdb file using ambpdb command.
> > But it shows error:
> > ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0..
>
> You don't say what arguments you gave to ambpdb. The number of atoms
> is the first integer at the top of the prmtop file, and the first integer
> at the top of the restart file. You can check manually to see if those
> are the same.
>
> If I had to guess (based on very limited information), you may have tried
> to use a trajectory file (rather than a restart file) as input to ambpdb.
> This will work for cpptraj but not for ambpdb.
>
> ....dac
>
>
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Received on Mon Oct 13 2014 - 14:00:03 PDT
