Dear Amber specialist,
I don't have any experience in checking hydrogen bonds but I
intend to check for changes in hydrogen bonds of a dimer protein (two
monomer with 55 aa) in protein-DNA complex with 170 residues (1-110 aa
& a 30-mer DNA (111-170)).
I created a .ptraj file (model.ptraj)
containing
trajin model_wat_md2.mdcrd 1
1000 5
trajout model_wat_md.mdcrd
center
:1-110
strip : WAT
go
and I issued the following command:
./ptraj
model_wat.prmtop < model.ptraj
then, to abstract hydrogen bonds I created
an .in file. Attached I am
sending the file. But when I issue the following command:
./ptraj model_wat.prmtop
<ptraj.1.in> ptraj.1.out
the
following message appear on screen and it last for a long time without any
action
checking coordinates:
/root/amber9/exe/model_md.mdcrd
Does it wrong?
what's wrong with me?
would you please help me?
Regards,
Ehsan
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Received on Wed Sep 01 2010 - 02:30:04 PDT
