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
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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Received on Sun Aug 26 2007 - 06:07:40 PDT
