AMBER Archive (2008)

Subject: AMBER: RESP charges of an unusual substrate

From: Jiayun Pang (Jiayun.Pang_at_manchester.ac.uk)
Date: Fri May 16 2008 - 05:45:54 CDT

Dear amber community,
I am doing MDs using amber FF94 and amber 9 to an enzyme with a rather
unusual substrate. Please see the attached pdb for the structure. I
have added NME and ACE to cap the N-H and C=O termini.

It has three TRP like residues that covalently bound to each other
(named as TTW, TTR and TRR in pdb).

My question is what's the best way to obtain the RESP charge for it?
Is it necessary to treat them as one unit, calculate ESP charge in
Gaussian, then fit the RESP using either antechamber or RED? I
suppose, with a structure as big as this, the final RESP charge will
be quite conformation-dependent.

Alternatively, to reduce the complexity, I could omit TRR and use the
charge of standard TRP residue for it. But how should I adjust the
charge of CG, CD1, NE1 to accommodate the loss of the H connected to
CD1.

Another thing is, TTR is exactly like the sidechain of TRP. Could I
apply similar charges of TRP for it as well?

I hope I have made myself clear.

Your advice will be really appreciated.

Best wishes,

Jiayun

==============================================================================
ATOM 1 CA ACE 38 5.162 19.533 -15.306 0.00 C
ATOM 2 H ACE 38 5.032 18.521 -15.024 0.00 H
ATOM 3 H ACE 38 5.485 20.094 -14.468 0.00 H
ATOM 4 HA ACE 38 5.910 19.597 -16.096 0.00 H
ATOM 5 C ACE 38 3.867 20.079 -15.795 0.00 C
ATOM 6 O ACE 38 3.748 20.516 -16.935 0.00 O
ATOM 7 O3 TTW 39 2.967 22.441 -13.624 0.00 O
ATOM 8 C23 TTW 39 2.099 22.327 -14.472 0.00 C
ATOM 9 C3 TTW 39 1.784 20.980 -15.101 0.00 C
ATOM 10 N1 TTW 39 2.881 20.085 -14.930 0.00 N
ATOM 11 4H TTW 39 3.632 20.395 -14.352 0.00 H
ATOM 12 5H TTW 39 1.697 21.197 -16.155 0.00 H
ATOM 13 C4 TTW 39 0.479 20.375 -14.578 0.00 C
ATOM 14 6H TTW 39 0.288 19.450 -15.159 0.00 H
ATOM 15 7H TTW 39 -0.329 21.109 -14.778 0.00 H
ATOM 16 C5 TTW 39 0.380 19.992 -13.073 0.00 C
ATOM 17 C6 TTW 39 -0.064 20.800 -12.095 0.00 C
ATOM 18 8H TTW 39 -0.391 21.819 -12.241 0.00 H
ATOM 19 N2 TTW 39 -0.046 20.158 -10.894 0.00 N
ATOM 20 9H TTW 39 -0.322 20.548 -10.043 0.00 H
ATOM 21 C7 TTW 39 0.416 18.890 -11.065 0.00 C
ATOM 22 C11 TTW 39 0.598 17.892 -10.135 0.00 C
ATOM 23 O2 TTW 39 0.319 18.130 -8.969 0.00 O
ATOM 24 C8 TTW 39 0.701 18.724 -12.414 0.00 C
ATOM 25 C9 TTW 39 1.195 17.479 -12.833 0.00 C
ATOM 26 C10 TTW 39 1.372 16.471 -11.872 0.00 C
ATOM 27 H TTW 39 1.745 15.505 -12.167 0.00 H
ATOM 28 C12 TTW 39 1.074 16.699 -10.549 0.00 C
ATOM 29 N3 TTW 39 1.243 15.757 -9.684 0.00
       N1+
ATOM 30 H TTW 39 1.906 15.874 -8.933 0.00 H
ATOM 31 C13 TTR 40 0.442 14.730 -9.979 0.00 C
ATOM 32 3H1 TTR 40 0.738 14.429 -11.004 0.00 H
ATOM 33 4H1 TTR 40 -0.579 15.162 -9.982 0.00 H
ATOM 34 C14 TTR 40 0.379 13.428 -9.126 0.00 C
ATOM 35 5H1 TTR 40 0.098 13.677 -8.080 0.00 H
ATOM 36 6H1 TTR 40 1.371 12.929 -9.128 0.00 H
ATOM 37 C15 TTR 40 -0.661 12.487 -9.717 0.00 C
ATOM 38 C16 TTR 40 -2.001 12.779 -9.937 0.00 C
ATOM 39 7H1 TTR 40 -2.485 13.719 -9.717 0.00 H
ATOM 40 N4 TTR 40 -2.602 11.682 -10.479 0.00 N
ATOM 41 8H1 TTR 40 -3.544 11.622 -10.726 0.00 H
ATOM 42 C17 TTR 40 -1.700 10.696 -10.622 0.00 C
ATOM 43 C18 TTR 40 -0.485 11.178 -10.147 0.00 C
ATOM 44 C22 TTR 40 0.641 10.392 -10.161 0.00 C
ATOM 45 2H2 TTR 40 1.588 10.762 -9.796 0.00 H
ATOM 46 C20 TTR 40 0.563 9.096 -10.653 0.00 C
ATOM 47 0H2 TTR 40 1.443 8.471 -10.665 0.00 H
ATOM 48 C21 TTR 40 -0.646 8.602 -11.131 0.00 C
ATOM 49 1H2 TTR 40 -0.700 7.595 -11.518 0.00 H
ATOM 50 C19 TTR 40 -1.780 9.396 -11.112 0.00 C
ATOM 51 9H1 TTR 40 -2.712 8.992 -11.479 0.00 H
ATOM 52 N NME 41 1.378 23.342 -14.926 0.00 N
ATOM 53 1H NME 41 1.471 23.137 -15.911 0.00 H
ATOM 54 CA NME 41 1.574 24.727 -14.483 0.00 C
ATOM 55 H NME 41 1.416 24.789 -13.438 0.00 H
ATOM 56 H NME 41 2.562 25.034 -14.710 0.00 H
ATOM 57 HA NME 41 0.889 25.425 -14.966 0.00 H
ATOM 58 CA ACE 89 1.497 11.687 -13.271 0.00 C
ATOM 59 H ACE 89 0.644 12.296 -13.122 0.00 H
ATOM 60 H ACE 89 1.909 11.421 -12.332 0.00 H
ATOM 61 HA ACE 89 1.209 10.784 -13.810 0.00 H
ATOM 62 C ACE 89 2.534 12.474 -14.060 0.00 C
ATOM 63 O ACE 89 2.918 12.054 -15.140 0.00 O
ATOM 64 N TRR 90 3.004 13.608 -13.542 0.00 N
ATOM 65 H TRR 90 2.550 14.051 -12.758 0.00 H
ATOM 66 CA TRR 90 3.984 14.362 -14.279 0.00 C
ATOM 67 HA TRR 90 3.802 14.233 -15.346 0.00 H
ATOM 68 CB TRR 90 3.929 15.892 -13.944 0.00 C
ATOM 69 2HB TRR 90 3.718 16.054 -12.888 0.00 H
ATOM 70 3HB TRR 90 4.820 16.455 -14.226 0.00 H
ATOM 71 CG TRR 90 2.790 16.489 -14.704 0.00 C
ATOM 72 CD1 TRR 90 1.604 16.999 -14.219 0.00 C
ATOM 73 NE1 TRR 90 0.806 17.409 -15.252 0.00 N
ATOM 74 1HE TRR 90 -0.116 17.815 -15.169 0.00 H
ATOM 75 CE2 TRR 90 1.472 17.177 -16.426 0.00 C
ATOM 76 CZ2 TRR 90 1.093 17.432 -17.725 0.00 C
ATOM 77 2HZ TRR 90 0.113 17.878 -17.896 0.00 H
ATOM 78 CH2 TRR 90 1.971 17.108 -18.720 0.00 C
ATOM 79 2HH TRR 90 1.700 17.304 -19.757 0.00 H
ATOM 80 CZ3 TRR 90 3.199 16.537 -18.445 0.00 C
ATOM 81 3HZ TRR 90 3.890 16.277 -19.247 0.00 H
ATOM 82 CE3 TRR 90 3.587 16.278 -17.146 0.00 C
ATOM 83 3HE TRR 90 4.577 15.854 -16.983 0.00 H
ATOM 84 CD2 TRR 90 2.713 16.596 -16.103 0.00 C
ATOM 85 C TRR 90 5.380 13.715 -14.249 0.00 C
ATOM 86 O TRR 90 6.295 14.215 -14.883 0.00 O
ATOM 87 N NME 91 5.505 12.574 -13.550 0.00 N
ATOM 88 H NME 91 4.736 12.271 -12.969 0.00 H
ATOM 89 CA NME 91 6.667 11.687 -13.684 0.00 C
ATOM 90 H NME 91 6.742 11.352 -14.686 0.00 H
ATOM 91 H NME 91 7.546 12.215 -13.421 0.00 H
ATOM 92 HA NME 91 6.558 10.824 -13.026 0.00 H
TER

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