---------- Forwarded message ----------
From: siddesh southekal <siddeshonline.gmail.com>
Date: Mon, Apr 11, 2011 at 5:04 PM
Subject: docked complex file preparation
To: AMBER Mailing List <amber.ambermd.org>
hello ,
I have a doubt about generating the ( protein-ligand ) complex file .
I used AutoDock to get various poses of the ligand at the binding site .I
then inserted the coordinates of the ligand into the pdb file of the protein
to generate a complex.
(extracted the ligand coordinates from dlg file and saved in pdb format ).
I futhur used antechamber to generate the missing parameters for the ligand.
and finally generated the .top and .crd files for the complex using t-leap.
I do not get any errors here.
But when i do the equilibration step , i observe that the .rst file
generated is incomplete ( or has gaps ) and pmemd crashes (error msg :
pmemd terminated abruptly ).I have attached the .rst file generated
(complex_eqi.rst).
However it runs fine at the previous steps -minimisation and heating .I used
ntx=1and irest=0 .I checked the restart file which i used as input and it
looks alright , with the box information.
I did not have such problem when i used the protein wihtout the ligand ,Do
you think that this caused due to error in the way i have produced the
docked complex file .If so please let me know the steps.
Any suggestions would be helpful
thanks
sid
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Received on Tue Apr 12 2011 - 19:30:03 PDT
