Hi Amber users:
I am trying to derive RESP charges for prontonated cytosine ribonucleotide (N3 atom). According to Cieplak¡¯s work (1995, JCC), I constructed protonated cytosine nucleoside and performed optimization of geometry at MP2/6-31G(d) level using Gaussian09E.01. Then the optimized structure with sugar in C3¡¯ endo conformation was used for ESP calculation at HF/6-31G(d) level.
I tried 3 types of RESP fitting scheme using Antechamber or resp tool (Amber16). In the case of first method, the RESP fitting was performed using Antechamber with default set, where no additional restraint was employed (resp1). In the second, the charges on sugar atoms except C1¡¯ and H1¡¯ were kept frozen to the values in Amber99, and one stage fitting was performed using resp program to obtain the charge for the other atoms (resp2). In scheme 3, the total charge of sugar atoms except C1¡¯ and H1¡¯ were restrained to a value (-0.117e, identical to the net charge of fragment in Amber99) during two stage fit.
My concern is whether the charges on C1¡¯ and H1¡¯ atom (table1) derived from my calculation appear to be slight high from electrostatic point of view? Is it appropriate to use the charges on base together with C1¡¯ and H1¡¯ atoms derived from scheme 3 (resp3) in MD simulation with amber99 force field.
Additionally, I also performed the RESP fitting for non-protonated cytosine nucleoside using similar methods. For both form of protonated and non-protonated, the input geometries for ESP calculation are in A-form conformation and only conformation was employed. Compared to the parameters in Amber99 (see table 2), the charges on the atoms close to the bond of C1¡¯-N1 based on RESP scheme 2 and 3 seem too high. My third question is how can I eliminate the large fluctuation of charges on these atoms? Any suggestion and advice would be appreciated. Thanks in advance.
With regard
Xuzhh
Table 1 charge for protonated cytosine ribonucleoside
#id atom esp resp1 resp2 resp3
1 O5' -0.691411 -0.683438 -0.623300 -0.682630
2 H5T 0.456630 0.455464 0.429500 0.455277
3 O3' -0.702400 -0.691657 -0.654100 -0.691153
4 H3T 0.462249 0.459708 0.437600 0.459455
5 C3' 0.268134 0.254500 0.202200 0.254247
6 H3' 0.005528 0.016955 0.061500 0.017206
7 C4' 0.310030 0.269774 0.106500 0.267077
8 H4' 0.062754 0.080404 0.117400 0.081338
9 C5' 0.124194 0.102584 0.055800 0.101935
10 H5'1 0.063847 0.063623 0.067900 0.063874
11 H5'2 0.046771 0.063623 0.067900 0.063874
12 O4' -0.524952 -0.484444 -0.354800 -0.480709
13 C1' 0.375829 0.259909 0.497965 0.249365
14 H1' 0.130605 0.154501 0.047720 0.157073
15 C2' 0.060475 0.066401 0.067000 0.069761
16 H2'1 0.070224 0.074224 0.097200 0.073725
17 O2' -0.633340 -0.618750 -0.613900 -0.618213
18 HO'2 0.455154 0.448509 0.418600 0.447936
19 N4 -1.135793 -1.079714 -1.129145 -1.079141
20 H41 0.519949 0.505643 0.523404 0.505493
21 H42 0.514235 0.505643 0.523404 0.505493
22 C4 1.120460 0.976086 0.968262 0.975508
23 N3 -0.754308 -0.635010 -0.607217 -0.635146
24 H3 0.427890 0.406446 0.392668 0.406541
25 C2 0.797537 0.678703 0.735527 0.678515
26 O2 -0.522145 -0.499654 -0.511191 -0.499559
27 N1 -0.355121 -0.187211 -0.346964 -0.183910
28 C6 0.411731 0.255221 0.096594 0.255389
29 H6 0.186705 0.218567 0.265200 0.217987
30 C5 -0.842686 -0.705816 -0.580809 -0.705942
31 H5 0.291225 0.269207 0.241583 0.269335
RMSE na 0.068545 0.105540 0.069631
Table 2 charge on cytosine ribonucleoside
#id atom amber99 esp resp1 resp2 resp3
1 O5' -0.622300 -0.675638 -0.672089 -0.623300 -0.654321
2 H5T 0.429500 0.441093 0.440972 0.429500 0.437311
3 O3' -0.654100 -0.699582 -0.697714 -0.654100 -0.682394
4 H3T 0.437600 0.443024 0.443055 0.437600 0.435087
5 C3' 0.202200 0.216820 0.211236 0.202200 0.207612
6 H3' 0.061500 0.030168 0.032471 0.061500 0.040514
7 C4' 0.106500 0.353857 0.353783 0.106500 0.259370
8 H4' 0.117400 0.028195 0.031011 0.117400 0.062152
9 C5' 0.055800 0.124476 0.113384 0.055800 0.101773
10 H5'1 0.067900 0.046954 0.038980 0.067900 0.045150
11 H5'2 0.067900 0.025107 0.038980 0.067900 0.045150
12 O4' -0.354800 -0.563753 -0.558305 -0.354800 -0.442914
13 C1' 0.006600 0.453430 0.421260 0.094890 0.095033
14 H1' 0.202900 0.084596 0.094364 0.167810 0.174105
15 C2' 0.067000 0.088958 0.087899 0.067000 0.189298
16 H2'1 0.097200 0.070734 0.074668 0.097200 0.059630
17 O2' -0.613900 -0.655210 -0.651858 -0.613900 -0.637068
18 HO'2 0.418600 0.434283 0.433093 0.418600 0.416649
19 N4 -0.953000 -0.971342 -0.963806 -0.942767 -0.956846
20 H41 0.423400 0.396721 0.403485 0.397436 0.402412
21 H42 0.423400 0.414256 0.403485 0.397436 0.402412
22 C4 0.818500 1.013795 0.992773 0.964965 0.975538
23 N3 -0.758400 -0.882286 -0.852120 -0.859502 -0.846588
24 C2 0.753800 0.932632 0.895589 0.892140 0.883283
25 O2 -0.625200 -0.644739 -0.638851 -0.616521 -0.634376
26 N1 -0.048400 -0.407453 -0.372818 -0.264433 -0.263118
27 C6 0.005300 0.264043 0.255140 0.244043 0.251176
28 H6 0.195800 0.175094 0.177567 0.152573 0.167522
29 C5 -0.521500 -0.792088 -0.785123 -0.757506 -0.785947
30 H5 0.192800 0.253854 0.249490 0.246436 0.252394
RMSE na 0.153088 0.142345 0.126908# 0.099378
# non-frozen atoms
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 29 2017 - 04:00:02 PDT
