Carlos has the right idea for triage - see if it happens without GB, and
if so, then concentrate on the force field.
> some ligands with the same ring do not bind to Zn2+ but still the
aromatic ring plane is distorted during the simulation
Do you mean standard residues distort in the same way, even when not
next to a Zn2+?
If it's due to the 2+ charge I think adding impropers could be worth a
try, but I'd expect to have heard this problem before in this case, so
not sure.
> Btw, why the radius of both Zn2+ and Mg2+ is 1.5 A. when measured in VMD? Shouldn't they be different?
I doubt VMD is using prmtop values - just defaulting, as one often does.
Bill
On 9/16/16 4:03 AM, Thomas Evangelidis wrote:
> I need some advice about GB simulations of a protein-ligand complex with
> Zn2+ ion. No matter which GB model I use, the aromatic pentameric ring
> binds to the ion and becomes distorted, as shown in these photos:
>
> https://dl.dropboxusercontent.com/u/48168252/ligand2.png
>
> https://dl.dropboxusercontent.com/u/48168252/pentamer_ring.png
>
>
> The frcmod of the ligand looks like this:
>
>
> remark goes here
>> MASS
>> BOND
>> n1-cc 536.50 1.311 same as ce-n1
>> ANGLE
>> n1-nd-cd 75.270 115.090 same as c2-n2-n1
>> n1-cc-nc 75.888 118.985 Calculated with empirical approach
>> n1-cc-h5 51.660 121.535 Calculated with empirical approach
>> *nd-n1-cc 0.000 0.000 ATTN, need revision*
>> DIHE
>> IMPROPER
>> c3-nc-cd-nd 1.1 180.0 2.0 Using default
>> value
>> h5-n1-cc-nc 1.1 180.0 2.0 Using default
>> value
>> NONBON
>
>
> I don't think that the missing angle is the problem, neither the charges
> because some ligands with the same ring do not bind to Zn2+ but still the
> aromatic ring plane is distorted during the simulation. Do you believe than
> the impropers are insufficient and I must add more? Has anyone observed the
> same artifact in GB simulations?
>
> Btw, why the radius of both Zn2+ and Mg2+ is 1.5 A. when measured in VMD?
> Shouldn't they be different?
>
> I would be grateful for any advice.
> Thomas
>
>
>
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Received on Fri Sep 16 2016 - 10:30:02 PDT
