I'm trying to calculate RESP charges of atoms in a complex system. I need to keep a fixed charge on certain atoms during the charge calculation. Is there any such procedure in REDtools or REDserver?
I was trying to give few charge restraints in the Project.config file as,
MOLECULE1-INTRA-MCC1 = -0.834 | 46 49 52 55 58 61| K
MOLECULE1-INTRA-MCC1 = 0.417 | 47 48 50 51 53 54| K
MOLECULE1-INTRA-MCC1 = 0.417 | 56 57 59 60 62 63| K
The same atoms show different charges in the PyRED output file,
-0.8121
0.4226 respectively
Charges have changed even the restraints were imposed.
Is there any problem related to the calculation?
Yes, I need to check it carefully. The changes are provided in the Statistics_m1.txt file.
46 O8 -0.8121 -0.8586 0.0465
47 H3 0.4226 0.4347 -0.0121
48 H4 0.4226 0.4023 0.0203
So, I kept constraints on charges of atoms in coordinated water molecules. Actually, my system has Mg2+ and a nucleotide analogue with phosphate moiety.
I performed this calculation in PyRED (development version) and did not do it in the old RED server. I think I should check it once in the old one. Thanks
While optimizing the Mg2+ bound nucleotide (Phosphate) in Gaussian, I saw the Mg-O distances were decreased about ~0.2-0.3 Ang from the distances present in crystal structure.
There are water molecules (octahedral coordination) bound to the Mg2+. So, we thought that optimizing Mg-Nuc alone would not provide correct geometry of the moiety. Optimizing the whole complex resulted a good structure. This optimized structure was then submitted to PyRED server with the charge constrains on water molecules. The point is, classically there should not be any charge transfer (neutral water) from Mg2+ to TIP3P water.
Basically, I've got the intuition after going through this paper
http://pubs.acs.org/doi/abs/10.1021/ja210656k
Although, they did not include water molecules in their calculations.
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