AMBER Archive (2009)

Subject: [AMBER] implicit solvent MD with fixed residues

From: Hakan Gunaydin (gunaydih_at_yahoo.com)
Date: Thu Dec 24 2009 - 17:43:13 CST

Dear Amber users,

I am trying to run a MD job with some residues allowed to move and others fixed. I understand that I need to move the residues that are allowed to move to the top of the pdb file. I can do this for moving residues and run my MD job without any problem. However, I would like to be able to let some (crystallographic) water molecules and ligand to be allowed to move as well. This is where I have my problems. When I load my pdbfile to tleap and check the sequence; I get the following info:

R<LEU 84>
R<GLY 85>
R<ARG 86>
R<VAL 87>
R<GLY 88>
R<PRO 89>
R<WAT 90>
R<ACE 91>
R<VAL 92>
R<HID 93>
R<GLU 94>
R<NME 95>

As you can see; my moving resides and one water molecule is at the top of my loaded pdb file. I noticed that water molecule was moved to the bottom of the pdb file when I save the amberparm file in tleap. I haven't tried this with a ligand yet but I suppose I'll run into the same problem.

Can you please tell me how am I supposed to prevent tleap from reordering my pdb file?

Thanks,
-Hakan

      

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