On Mon, Oct 13, 2014, Hirdesh Kumar wrote:
> 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?
Yes: ambpdb only knows about formatted restart files. I think Dan has a
script that emulates the ambpdb functionality, but actually runs things
through cpptraj. It's probably time to get that out to users.
....dac
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Received on Mon Oct 13 2014 - 18:30:02 PDT
