AMBER Archive (2005)

Subject: AMBER: RESP of negatively charged molecule

From: Rhoad, Jonathan S. (rhoadj_at_missouri.edu)
Date: Tue Mar 01 2005 - 15:39:05 CST

I was attempting to obtain RESP charges for glucose-6-phosphate. I have
included the method and optimized geometry below. The structure was
optimized at mp2/6-31+G* with PCM (without PCM a proton migrated to the
phosphate). When I use antechamber or the resp(gen) programs
individually, I get the same nonsense charges. The prep file is after
the Gaussian input file.

 

antechamber -i output.log -fi gout -o g6p.prep -fo prepi -rn G6P -at
amber -c resp

 

where output.log is the output of the Gaussian file included.

 

Any suggestions? Would the ESP charges output in the Gaussian file be
good enough? I am trying to simulate the dynamic motion of sugar
phosphates in the active site of enzymes.

 

Thanks,

Jonathan Rhoad

University of Missouri

 

 

# hf/6-31+G(d) sp pop=mk scf=tight IOp(6/33=2)

 

-2 1

C -2.218496 -1.514421 0.250925

C -2.841025 -0.236926 0.810923

C -2.456779 0.955423 -0.051291

C -0.948398 0.992892 -0.228695

C -0.429008 -0.326598 -0.783213

C 1.074543 -0.354423 -0.931119

O -2.860871 -1.763714 -0.980495

O -4.247791 -0.385538 0.970549

O -2.922062 2.136351 0.601125

O -0.658237 2.074725 -1.122705

O -0.809237 -1.390773 0.116253

O 1.692802 0.083376 0.267180

P 3.404618 -0.066814 0.273953

O 3.873914 0.726611 -0.958070

O 3.668239 -1.580765 0.194876

O 3.740833 0.577286 1.628032

H -2.363305 -2.350348 0.948609

H -2.438877 -0.073120 1.819327

H -2.927300 0.855711 -1.044632

H -0.489311 1.167197 0.753295

H -0.879028 -0.504575 -1.771736

H 1.386325 -1.379133 -1.177377

H 1.356781 0.294608 -1.771237

H -2.617198 -2.682830 -1.264005

H -4.617197 -0.572358 0.075266

H -2.609697 2.891499 0.049849

H 0.223790 2.439407 -0.865811

 

    0 0 2

 

This is a remark line

molecule.res

G6P XYZ 0

CORRECT OMIT DU BEG

  0.0000

   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000

   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000

   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000

   4 O4 OH M 3 2 1 1.540 111.208 180.000 1.224

   5 H11 HO E 4 3 2 0.993 152.287 -148.100 0.430

   6 C4 CT M 4 3 2 1.436 78.469 -39.722 -1.121

   7 H4 H1 E 6 4 3 1.099 110.233 -122.639 2.167

   8 C3 CT M 6 4 3 1.521 106.979 -4.616 -13.618

   9 O3 OH S 8 6 4 1.432 111.076 -65.289 2.625

  10 H10 HO E 9 8 6 0.991 107.756 58.034 1.309

  11 H3 H1 E 8 6 4 1.103 109.191 55.801 5.178

  12 C2 CT M 8 6 4 1.523 109.444 176.132 -2.363

  13 O2 OH S 12 8 6 1.428 113.121 -177.859 0.955

  14 H9 HO E 13 12 8 0.992 108.656 63.148 2.084

  15 H2 H1 E 12 8 6 1.099 108.379 65.602 3.678

  16 C1 CT M 12 8 6 1.529 110.650 -52.563 -12.046

  17 O1 OH S 16 12 8 1.413 106.989 -68.254 0.310

  18 H8 HO E 17 16 12 0.996 108.491 -167.564 2.299

  19 H1 H2 E 16 12 8 1.098 110.642 170.717 4.529

  20 O5 OS M 16 12 8 1.424 111.048 54.580 3.759

  21 C5 CT M 20 16 12 1.446 113.172 -59.830 -0.233

  22 H5 H1 E 21 20 16 1.101 109.345 -58.210 1.798

  23 C6 CT M 21 20 16 1.512 107.769 -175.474 -5.644

  24 H6 H1 E 23 21 20 1.099 108.599 49.872 1.605

  25 H7 H1 E 23 21 20 1.099 108.881 167.584 1.605

  26 O6 OS M 23 21 20 1.426 109.774 -71.486 0.182

  27 P1 P M 26 23 21 1.710 116.411 173.721 -5.788

  28 O8 O E 27 26 23 1.550 105.802 -64.142 1.691

  29 O9 O E 27 26 23 1.548 101.227 176.266 1.691

  30 O7 O M 27 26 23 1.551 105.534 56.542 1.691

 

 

LOOP

   C5 C4

 

IMPROPER

 

DONE

STOP

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