RE: AMBER: Cyclohexane solvent Box

From: Ross Walker <>
Date: Mon, 17 Oct 2005 07:03:54 -0700

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

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Mon Oct 17 2005 - 15:53:00 PDT
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