AMBER Archive (2005)

Subject: Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production?

From: Thomas Cheatham (
Date: Tue Nov 22 2005 - 22:35:11 CST

> One more question, When i use the following script:
> I found there is sth wrong with the output pdb file. When i open the
> closest1.pdb by VMD, some residues are separated or bonds are missing.

What is "sth"; is this short for something?

You will have to describe to me in greater detail what you are seeing. Is
the solvent incorrectly specified? Are TER cards missing between residues
(ptraj does not add TER cards at present). Were atoms truncated?

The PDB you show does not help me since I have no idea what residues are
what nor can I possibly know what atoms are missing...

I will assume that ACN is your solvent; if you defined this as such in
ptraj and a wrong PDB was output, I should know about this...

> If I output the file in trj format, how can i get the NEW prmtop file from the
> trj file for the residues with selected solvent molecules?

To look at the new trajectory, you need a new prmtop file which as exactly
as many solvent residues (and solute in the same order as previous) as you
specified with the closest. If the solvent is water, you can use the
undocumented testwater command to rdparm to generate an old style prmtop.
If not, you have to either solvatebox or solvateoct iteratively until you
get an exact match with the number of solvents or read in a PDB with the
solvent (of the same size) and use the setbox command to specify box

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