John,
> Thank you. My molecule is composed a direct binding of sugar at C1
> and the lysine (NZ). The nitrogen atom has a single hydrogen atom.
> Please, I have still more questions, should I copy CT-N3- CT in
> frcmod as text. and should I apply ff99SB and Glycam_06h together or
> only ff99SB at leap. I attached my file as FUL.mol2.
I looked your this FUL.mol2 file:
- First you have a strange atom connectivity and an open valency for
the NH connected to the alpha-carbon connected to the carboxylate
group. Cartesian coordinates do not matter in a FF library but if you
use R.E.D. III.x (above III.4) or R.E.D.Server/R.E.D. IV the geometry
of a fused connection between two different fragments should be well
constructed/look 'pretty'.
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php#4
So this likely means that something wrong append; but where?
- Then, you have a secondary amine; thus I think you should:
NOT use:
HP
Lys-CT-N3-Cg-sugar
HP H
but USE:
H1 H1 O H1
Lys-CT-NT-Cg-C-Cg-...
H1 H H1 OH
HO
- then, this type of connection:
O
-CH2-N-CH2-C-
H
is quite unusual; I hope the constraints applied during the charge
fitting step did not break the fit. you can use the private assistance
service at R.E.D. Server;
see
http://q4md-forcefieldtools.org/REDS/help-log.php
so that we can help you to construct your connection...
- Finally your sugar is not cyclic, but this is an 'linear' form: I am
not sure associating the last version of the Amber FF + a Glycam
version i/h/z? is the best choice: this looks like quite complicated
for a first approach. I am sure parm99.dat by itself handles this
bio-organic molecule. Then, you can try to adapt key dihedral FF
parameters if this is required...
regards, Francois
>> Date: Thu, 17 Jan 2013 08:57:27 +0100
>> From: fyd.q4md-forcefieldtools.org
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] A link atoms between protein and sugar!
>>
>> Dear John,
>>
>> > I built a protein-sugar complex. The lysine residue (NZ atom) is
>> > involved in the binding to sugar (C1 atom). I separated lysine-sugar
>> > residue to generate a library for this complex. I used R.E.D server
>> > to assign its charges and get a FUL.mol2 file. The problem is, I
>> > can do not no how can I parameterize the angle CT-N3-Cg, a bond
>> > between a GLYCAM_06h
>> > atom type and an amber atom type. Please, can I get any suggestions.
>>
>> The atom type for NZ of LYS is N3 (& the atom type of HE (connected to
>> carbon CE) is HP) because NZ is an ammmonium group.
>>
>> What is this connection? is it a peptide bond?
>>
>> -> if yes, you end up with:
>> H1 O HC
>> Lys-CT-N-C-Cg-Cg-Sugar
>> H1 H HC
>> or
>> H1 O H1
>> Lys-CT-N-C-Cg-OS-Sugar
>> H1 H H1
>>
>> -> if no, I guess you need up with a secondary amine (or send a
>> drawing of this connection):
>> H1 H1
>> Lys-CT-NT-Cg-Cg-Sugar
>> H1 H H1
>> or
>> H1 H2
>> Lys-CT-NT-Cg-OS/Os-Sugar
>> H1 H H2
>>
>> if you only need CT-N3-Cg; this the same than CT-N3-CT (copy it in a
>> frcmod file); but I do not think you should use N3; if you have an
>> amine (& not an ammonium) you should use NT (& consequently H1 for HE
>> connected to CE).
>> see $AMBERHOME/data/leap/parm/parm99.dat
>> N3 14.01 0.530 sp3 N for charged amino groups
>> (Lys, etc)
>> NT 14.01 0.530 sp3 N for amino groups amino groups
>> -> There are errors in many Amber force field topology databases and
>> confusion between N3 & NT.
>>
>> I think once again here that using a black box strategy to assign atom
>> types is not a good idea; better understanding what you do...
>>
>> regards, Francois
>>
>> PS Please carefully check those new atom types in this GLYCAM...
>> h?i?z? version; I have no idea what they mean... I guess CG became Cg
>> & I guess H1 remains H1...
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Received on Thu Jan 17 2013 - 01:30:04 PST
