AMBER Archive (2007)

Subject: RE: AMBER: solvateCap minin and mdin for qm-mm dftb

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Aug 24 2007 - 08:10:54 CDT

Hi Francesco,

>solvateCap EQE TIP3PBOX EQE 20.0

Try:

 tleap

 source leaprc.ff99SB
 NMA = sequence { ACE NME }
 desc NMA
 UNIT name: ACE
 Head atom: null
 Tail atom: null
 Contents:
 R<ACE 1>
 R<NME 2>

So say we want the solvent cap centered on an atom in the NME residue:

 desc NMA.2

 RESIDUE name: NME
 RESIDUE sequence number: 2
 RESIDUE PDB sequence number: 2
 Type: protein
 Connection atoms:
 Connect atom 0: A<N 1>
 Connect atom 1: A<CH3 3>
 Improper torsions:
 Contents:
 A<HH33 6>
 A<HH32 5>
 A<HH31 4>
 A<CH3 3>
 A<H 2>
 A<N 1>

So say we want the CH3 atom (Atom 3 of residue 2) as the center of our cap
and we want a 10A radius cap of TIP3P water then we would use:

 help solvatecap

    solvateCap solute solvent position radius [ closeness ]

So:

 solvatecap NMA TIP3PBOX NMA.2.3 10.0
 Added 103 residues.

And there you have it...

> That said, on summing up info from the manual and suggestions
> from Bud and
> Gustavo, I have a number of doubts about min.in and md.in,
> in particular if
> qm_pme should be omitted at all. The two files I have set up read:

If ntb=0 (which you will need for a solvent cap since there are no periodic
boundaries) then qm_ewald and qm_pme are ignored so you don't need to
specify them. Note you will likely want a much much bigger cutoff - say 14
to 16 angstroms or even 999.0 (ca. infinite) since you have no PME in play
here.

All the best
Ross

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|\oss Walker

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| San Diego Supercomputer Center |
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