Dear Denis,
> I read the paper "Molecular dynamics studies of native and
> substituted cyclodextrins in different media: 1. Charge derivation and
> force field performances" in Phys. Chem. Chem. Phys., 2011,13,
> 15103-15121, and download the whole project from
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/ as describe in
> the paper.
All is summarized in the script:
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
> I want to preform a MD with an unsubstituted beta-cyclodextrin, How
> can I apply the q4md-CD forcefield to my molecules? Is there any
> tutorial or example?
For unsubstituted beta-cyclodextrin, look for Summarize a-, b- and
g-cyclodextrin names:
per-OH b-CD = BCDOH
# per-OH beta-cyclodextrin
BCDOH = seq {MGO MGO MGO MGO MGO MGO MGO}
set BCDOH head BCDOH.1.C4
set BCDOH tail BCDOH.7.O1
i BCDOH {1 2 3 4 5 6 7} {{O5 C1 O1 C4 98.0}{C1 O1 C4 C5 -103.00}}
bond BCDOH.1.C4 BCDOH.7.O1
So it looks like you only need the fragment: MGO = loadmol2 tripos7.mol2
let us know if you need more help...
regards, Francois
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Received on Mon Nov 05 2012 - 14:00:03 PST
