I am preparing a protein that has a Zn finger for molecular dynamics.
To indicate the finger of Zn a patch is placed in which the deprotonation of the cysteines is necessary so that the Zn ion can join them but when the molecule is ionized the charges are not neutralized ... When I apply the comands it seems like it works but when I solvate and ionice the model I show a massage saying: "System has a non-integer total charge. there is a problem in process of building it" .so I cannot continue with The minimization.
Could someone help me with this problem of the charges?
Currently I´m trying the following the force fields
topology topology/top_all27_prot_lipid.inp topology topology/toppar_all22_prot_zincpatchCYSD.txt topology topology/toppar_all22_prot_zincpatch.txt
I will be very grateful for your help.
Cheers.
I would like to suggest you some useful links to follow: Article A theoretical investigation of DNA dynamics and desolvation ...
Article Structural Basis of the Disorder in the Tandem Zinc Finger D...
Article Molecular dynamics simulations of the glucocorticoid recepto...
I guess you have done some modifications with the protonation state of your system after the solvation and addition of ions, which moved your system to the non-neutral state. Based on the total charge (at present) of your system you can delete positive/negative ions (for example K and Cl ion, I don't know which ions you have added to your system to neutralize); suppose your system currently has charge -1.000, so you can delete a Cl ion from the .gro/.pdb file (if .gro, remember to reduce the total number of atom at the beginning of file) and reduce the number of CL ion in .top file by one.
I hope it will solve the issue!
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