Dear Prof. Francois,
I read the script1.ff, but still have some question. For
example, if I want to apply q4md-CD to a existing PDB file, such as
BUVSEQ02 from CSD database. I modified the atom name of each residue
in PDB file as in tripos7.mol2. Does the following tleap script work?
In the script1.ff,
Q4MDCD = loadamberparams frcmod.q4md
Should I replace frcmod.q4md with script3.ff ?
I am using Amber12, which did not include Glycam04, There are
Glycam04_a,Glycam04_b …… Glycam04_k, Glycam04_l in official website,
http://glycam.ccrc.uga.edu/ccrc/pages/parameters.html, which one
should I download?
As described in the PCCP paper, there are scaling factors of 1.2 and
2.0 were imposed for the 1–4 electrostatic and 1–4 van der Waals
interactions in q4md_CD force field, will it work well when there are
other molecules in the system?
###### start of leap script #######
addAtomTypes {
# Amber
{ "HZ" "H" "sp3" }
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "OW" "O" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "S" "S" "sp3" }
{ "CT" "C" "sp3" }
{ "CZ" "C" "sp3" }
{ "C" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "N" "N" "sp2" }
{ "CL" "Cl" "sp3" }
# Glycam
{ "CG" "C" "sp3" }
}
parm99 = loadamberparams parm99.dat
FF99SB = loadamberparams frcmod.ff99SB
CHCL3 = loadamberparams frcmod.chcl3
loadoff all_amino94.lib
loadoff all_aminoct94.lib
loadoff all_aminont94.lib
loadoff solvents.lib
# Use Glycam
glycam04 = loadamberparams glycam04.dat
HOH = TP3
WAT = TP3
Q4MDCD = loadamberparams frcmod.q4md
MGO = loadmol2 tripos7.mol2
set MGO name "MGO"
set MGO head MGO.1.C4
set MGO tail MGO.1.O1
set MGO.1 connect0 MGO.1.C4
set MGO.1 connect1 MGO.1.O1
set MGO.1 restype saccharide
set MGO.1 name "MGO"
# set FF atom types
set MGO.1.C1 type CG
set MGO.1.H1 type H2
set MGO.1.O1 type OS
set MGO.1.C2 type CG
set MGO.1.H2 type H1
set MGO.1.O2 type OH
set MGO.1.HO2 type HO
set MGO.1.C3 type CG
set MGO.1.H3 type H1
set MGO.1.O3 type OH
set MGO.1.HO3 type HO
set MGO.1.C4 type CG
set MGO.1.H4 type H1
set MGO.1.C5 type CG
set MGO.1.H5 type H1
set MGO.1.O5 type OS
set MGO.1.C6 type CG
set MGO.1.H61 type H1
set MGO.1.H62 type H1
set MGO.1.O6 type OH
set MGO.1.HO6 type HO
BCD = loadpdb BUVSEQ02.pdb
saveamberparm BCD bcd.top bcd.crd
######## end of leap script
2012/11/6 FyD <fyd.q4md-forcefieldtools.org>:
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Nov 06 2012 - 02:00:02 PST
