Re: AMBER: Cyclohexane solvent Box

From: chai ann ng <>
Date: Tue, 18 Oct 2005 00:27:13 +1000

Dear Rose,

I realized that but then the equilibrated model is dispersed, do you do
re-image on that? What is the general method of creating solvent box?
Is there a walk through guide available?


On 18/10/05 12:03 AM, "Ross Walker" <> wrote:

> Dear Andy,
>> I output the .rst to pdb file, but the cyclohexane molecule
>> is disperse. If
>> i read back into Leap, this is what happen. I have 117 residues. It
>> complaint the atoms are not in residue templates. And if I edit the
>> molecules, I only see boxes and it is without charges.
>> Creating new UNIT for residue: INT sequence: 117
>> Created a new atom named: C1 within residue: .R<INT 117>
> Did you build a library file for the residue named INT? In this case your
> cyclohexane? If you did then you need to load this into Leap before you load
> the pdb file that contains your cyclohexane solvent. It will then recognise
> the residue and give it the correct atom types and topology. Also, check
> that the name of the residue in the pdb file matches the residue name you
> used when you created the unit in the first place.
> If you didn't create a library file for it then you need to do this first
> before you can load the solvated pdb.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
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Received on Mon Oct 17 2005 - 15:53:00 PDT
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