Dear Liu Denis,
> 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?
A general rule: the _atom_ & _residue_ _names_ in the PDB file have to
match these in the FF library (the mol2 file).
In particular you can find in the script1.ff: set MGO.1.O1 type OS
-> this means that the exocyclic oxygene atom of the glycosidic bond
(i.e. the "O1" atom) belongs to the same residue than the "C1" atom ;
this is different from the GLYCAM approach. The residues have to be
split/named the same way in your PDB file.
> In the script1.ff,
> Q4MDCD = loadamberparams frcmod.q4md
> Should I replace frcmod.q4md with script3.ff ?
Yes
See
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
this is written;
# To be loaded after the addAtomTypes command !
# FRCMOD1 = loadamberparams frcmod.protected-CD
# FRCMOD2 = loadamberparams frcmod.CHCL3
# FRCMOD3 = loadamberparams frcmod.DMSO
# FRCMOD4 = loadamberparams frcmod.spec
# All in one file: i.e. script3.ff See here !!!!
Q4MDCD = loadamberparams frcmod.q4md
> 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?
I have no idea: I cannot understand this classification.
I will send to your private email the Glycam04 file we used...
> 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?
This is indeed the key: However, we did not install & we do not use
Amber 12 yet. From what I read, you 'might' have to modify the column
of comments in the dihedral angle section in the force field parameter
file(s) you use.
BTW I find that this is a quite strange choice that this "column of
comments" is now (new version of Amber) read as a "new FF parameter"...
See
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script3.ff
For instance:
DIHEDRAL
OS-CG-CG-OH 1 0.144 0.0 -3 From parm98
->
DIHEDRAL
OS-CG-CG-OH 1 0.144 0.0 -3 SCEE=1.2 SCNB=2.0 From parm98
However, I guess/hope if you do not add "SCEE=1.2 SCNB=2.0" in the FF
parameter file, the defaults are used & I hope these defaults are
"SCEE=1.2 SCNB=2.0" and NOT "SCEE=1.0 SCNB=1.0".
I guess also you can check in the pmemd or sander output that the
model "SCEE=1.2 SCNB=2.0" and/or "SCEE=1.0 SCNB=1.0" are/is used...
Thus, you have to test by yourself to see how q4md-CD works in Amber
12 because once again we do not use Amber 12 yet. Or just send other
emails in the Amber mailing list to get more help.
I hope this helps...
regards, Francois
PS Please, also consider that this 'q4md-CD' FF was mainly designed to
be used for gl'u'co-peptides. This also shows that a far more
homogeneous approach than this juxtaposed approach (i.e. "SCEE=1.2
SCNB=2.0" for the peptide part and "SCEE=1.0 SCNB=1.0" for the sugar
part) can be followed.
> 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
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Received on Wed Nov 07 2012 - 00:30:02 PST
