Hi,
I have solved this. If anyone has the same issue - I have manually edited
the atom names for SAH in the PDB file to match those in the mol2 file.
Completed the tleap script now without errors.
On Wed, Jul 22, 2020 at 2:43 PM JoAnne Babula <
babula.ridgelinetherapeutics.com> wrote:
> Hello,
>
> I am having problems when running the following tleap script to produce
> topology and rst files for a complex (protein + small molecule [MAQ] +
> co-factor [SAH]):
>
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> *source leaprc.protein.ff14SBsource leaprc.gaffloadamberparams
> SAH.frcmodloadamberparams MAQ.frcmodloadoff SAH.libloadoff MAQ.libcomplex =
> loadpdb X-hclean.pdb*
>
> Resulting as follows:
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> *Welcome to LEaP!(no leaprc in search path)Sourcing: ./complex.script-----
> Source:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.protein.ff14SB-----
> Source of
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.protein.ff14SB
> doneLog file: ./leap.logLoading parameters:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/parm/parm10.datReading
> title:PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNALoading
> parameters:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/parm/frcmod.ff14SBReading
> force field modification type file (frcmod)Reading title:ff14SB protein
> backbone and sidechain parametersLoading library:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/lib/amino12.libLoading
> library:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/lib/aminoct12.libLoading
> library:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/lib/aminont12.lib-----
> Source:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.gaff-----
> Source of /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/cmd/leaprc.gaff
> doneLog file: ./leap.logLoading parameters:
> /home1/apps/intel17/impi17_0/amber/16.0/dat/leap/parm/gaff.datReading
> title:AMBER General Force Field for organic molecules (Version 1.8, Mar
> 2015)Loading parameters: ./SAH.frcmodReading force field modification type
> file (frcmod)Reading title:remark goes hereLoading parameters:
> ./MAQ.frcmodReading force field modification type file (frcmod)Reading
> title:remark goes hereLoading library: ./SAH.libLoading library:
> ./MAQ.libLoading PDB file: ./X-hclean.pdb*
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> *-- residue 266: duplicate [ H2] atoms (total 2) Warning: Atom names in
> each residue should be unique. (Same-name atoms are handled by using
> the first occurrence and by ignoring the rest. Frequently
> duplicate atom names stem from alternate conformations in the PDB
> file.) Added missing heavy atom: .R<CLEU 264>.A<OXT 20>Created a new atom
> named: N within residue: .R<SAH 266>Created a new atom named: CA within
> residue: .R<SAH 266>Created a new atom named: CB within residue: .R<SAH
> 266>Created a new atom named: CG within residue: .R<SAH 266>Created a new
> atom named: SD within residue: .R<SAH 266>Created a new atom named: C
> within residue: .R<SAH 266>Created a new atom named: O within residue:
> .R<SAH 266>Created a new atom named: OXT within residue: .R<SAH 266>Created
> a new atom named: C5' within residue: .R<SAH 266>Created a new atom named:
> C4' within residue: .R<SAH 266>Created a new atom named: O4' within
> residue: .R<SAH 266>Created a new atom named: C3' within residue: .R<SAH
> 266>Created a new atom named: O3' within residue: .R<SAH 266>Created a new
> atom named: C2' within residue: .R<SAH 266>Created a new atom named: O2'
> within residue: .R<SAH 266>Created a new atom named: C1' within residue:
> .R<SAH 266>Created a new atom named: N9 within residue: .R<SAH 266>Created
> a new atom named: N7 within residue: .R<SAH 266>Created a new atom named:
> HA within residue: .R<SAH 266>Created a new atom named: HB1 within residue:
> .R<SAH 266>Created a new atom named: HB2 within residue: .R<SAH 266>Created
> a new atom named: HG1 within residue: .R<SAH 266>Created a new atom named:
> HG2 within residue: .R<SAH 266>Created a new atom named: H5'1 within
> residue: .R<SAH 266>Created a new atom named: H5'2 within residue: .R<SAH
> 266>Created a new atom named: H4' within residue: .R<SAH 266>Created a new
> atom named: H3' within residue: .R<SAH 266>Created a new atom named: HO3'
> within residue: .R<SAH 266>Created a new atom named: H2' within residue:
> .R<SAH 266>Created a new atom named: HO2' within residue: .R<SAH
> 266>Created a new atom named: H1' within residue: .R<SAH 266>Created a new
> atom named: H61 within residue: .R<SAH 266>Created a new atom named: H62
> within residue: .R<SAH 266> Added missing heavy atom: .R<SAH 266>.A<C13
> 24> Added missing heavy atom: .R<SAH 266>.A<C14 26>*
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> * Added missing heavy atom: .R<SAH 266>.A<N5 23> Added missing heavy
> atom: .R<SAH 266>.A<N2 17> Added missing heavy atom: .R<SAH 266>.A<C11
> 20> Added missing heavy atom: .R<SAH 266>.A<C12 21> Added missing heavy
> atom: .R<SAH 266>.A<C9 16> Added missing heavy atom: .R<SAH 266>.A<C10
> 18> Added missing heavy atom: .R<SAH 266>.A<N4 22> Added missing heavy
> atom: .R<SAH 266>.A<O3 11> Added missing heavy atom: .R<SAH 266>.A<C7 12>
> Added missing heavy atom: .R<SAH 266>.A<O5 15> Added missing heavy atom:
> .R<SAH 266>.A<O4 13> Added missing heavy atom: .R<SAH 266>.A<S1 5> Added
> missing heavy atom: .R<SAH 266>.A<C3 4> Added missing heavy atom: .R<SAH
> 266>.A<C1 2> Added missing heavy atom: .R<SAH 266>.A<O1 7> Added missing
> heavy atom: .R<SAH 266>.A<O2 8> total atoms in file: 4237 Leap added 36
> missing atoms according to residue templates: 19 Heavy 17 H /
> lone pairs The file contained 33 atoms not in residue templates*
>
> I have already loaded the frcmod and mol2 files for the SAH non-standard
> residue but it seems they were not recognized. Also, mol2 and frcmod for
> SAH were generated using a Gaussian 16rA.03 rev A.03 output gesp file.
> Please assist. The file contents are as follows:
>
> SAH.mol2:
> .<TRIPOS>MOLECULE
> SAH
> 46 48 1 0 0
> SMALL
> resp
>
>
> .<TRIPOS>ATOM
> 1 N1 4.7930 2.8050 -0.3140 n4 1 SAH
> -0.610549
> 2 C1 4.9980 1.6710 0.6690 c3 1 SAH
> 0.063241
> 3 C2 4.0070 0.5260 0.4660 c3 1 SAH
> -0.156260
> 4 C3 4.2170 -0.2590 -0.8310 c3 1 SAH
> 0.279216
> 5 S1 3.1240 -1.6960 -1.0460 ss 1 SAH
> -0.278619
> 6 C4 6.5020 1.2580 0.4940 c 1 SAH
> 0.803463
> 7 O1 7.1010 1.9630 -0.3360 o 1 SAH
> -0.741275
> 8 O2 6.8500 0.3230 1.1790 o 1 SAH
> -0.741275
> 9 C5 1.4950 -0.9300 -1.3280 c3 1 SAH
> -0.423766
> 10 C6 0.6010 -0.9530 -0.0970 c3 1 SAH
> 0.326755
> 11 O3 -0.5540 -0.1880 -0.3830 os 1 SAH
> -0.594334
> 12 C7 0.0990 -2.3540 0.3260 c3 1 SAH
> -0.073682
> 13 O4 0.2920 -2.5900 1.6960 oh 1 SAH
> -0.693896
> 14 C8 -1.4140 -2.2620 0.0920 c3 1 SAH
> 0.164159
> 15 O5 -2.1830 -3.0750 0.9010 oh 1 SAH
> -0.718555
> 16 C9 -1.6580 -0.7610 0.2660 c3 1 SAH
> 0.578746
> 17 N2 -2.8680 -0.2530 -0.3040 na 1 SAH
> -0.372947
> 18 C10 -3.2990 -0.3410 -1.6080 cc 1 SAH
> 0.349863
> 19 N3 -4.4060 0.2590 -1.8330 nd 1 SAH
> -0.638758
> 20 C11 -4.7560 0.7980 -0.6080 ca 1 SAH
> -0.047356
> 21 C12 -5.8470 1.5620 -0.1780 ca 1 SAH
> 0.819308
> 22 N4 -6.8310 1.9500 -1.0090 nh 1 SAH
> -0.975473
> 23 N5 -5.8960 1.9360 1.0950 nb 1 SAH
> -0.862961
> 24 C13 -4.9060 1.5750 1.9030 ca 1 SAH
> 0.677210
> 25 N6 -3.8370 0.8640 1.6200 nb 1 SAH
> -0.873988
> 26 C14 -3.8110 0.4950 0.3450 ca 1 SAH
> 0.634084
> 27 H1 4.1460 2.5970 -1.0550 hn 1 SAH
> 0.358704
> 28 H2 4.5120 3.6690 0.1180 hn 1 SAH
> 0.358704
> 29 H3 5.7630 2.8870 -0.6970 hn 1 SAH
> 0.358704
> 30 H4 4.8670 2.0890 1.6570 hx 1 SAH
> 0.094068
> 31 H5 2.9930 0.9120 0.5270 hc 1 SAH
> 0.076596
> 32 H6 4.1480 -0.1450 1.3030 hc 1 SAH
> 0.076596
> 33 H7 5.2160 -0.6750 -0.8440 h1 1 SAH
> 0.013433
> 34 H8 4.1200 0.3650 -1.7150 h1 1 SAH
> 0.013433
> 35 H9 1.0200 -1.4640 -2.1420 h1 1 SAH
> 0.176120
> 36 H10 1.6290 0.0930 -1.6590 h1 1 SAH
> 0.176120
> 37 H11 1.1150 -0.5100 0.7470 h1 1 SAH
> 0.062536
> 38 H12 0.5500 -3.1500 -0.2530 h1 1 SAH
> 0.195993
> 39 H13 1.1890 -2.8400 1.8740 ho 1 SAH
> 0.455561
> 40 H14 -1.6310 -2.5310 -0.9340 h1 1 SAH
> 0.111402
> 41 H15 -1.7680 -3.1600 1.7510 ho 1 SAH
> 0.489286
> 42 H16 -1.6780 -0.4960 1.3140 h2 1 SAH
> 0.073568
> 43 H17 -2.7290 -0.8640 -2.3480 h5 1 SAH
> 0.099654
> 44 H18 -7.6470 2.3600 -0.6130 hn 1 SAH
> 0.428860
> 45 H19 -6.8940 1.5480 -1.9160 hn 1 SAH
> 0.428860
> 46 H20 -4.9990 1.9090 2.9200 h5 1 SAH
> 0.059450
> .<TRIPOS>BOND
> 1 1 2 1
> 2 1 27 1
> 3 1 28 1
> 4 1 29 1
> 5 2 3 1
> 6 2 6 1
> 7 2 30 1
> 8 3 4 1
> 9 3 31 1
> 10 3 32 1
> 11 4 5 1
> 12 4 33 1
> 13 4 34 1
> 14 5 9 1
> 15 6 7 1
> 16 6 8 1
> 17 9 10 1
> 18 9 35 1
> 19 9 36 1
> 20 10 11 1
> 21 10 12 1
> 22 10 37 1
> 23 11 16 1
> 24 12 13 1
> 25 12 14 1
> 26 12 38 1
> 27 13 39 1
> 28 14 15 1
> 29 14 16 1
> 30 14 40 1
> 31 15 41 1
> 32 16 17 1
> 33 16 42 1
> 34 17 18 1
> 35 17 26 1
> 36 18 19 2
> 37 18 43 1
> 38 19 20 1
> 39 20 21 ar
> 40 20 26 ar
> 41 21 22 1
> 42 21 23 ar
> 43 22 44 1
> 44 22 45 1
> 45 23 24 ar
> 46 24 25 ar
> 47 24 46 1
> 48 25 26 ar
> .<TRIPOS>SUBSTRUCTURE
> 1 SAH 1 TEMP 0 **** **** 0 ROOT
>
>
>
> SAH.frcmod:
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> c3-o -c -o 1.1 180.0 2.0 General
> improper torsional angle (1 general atom type)
> c3-ca-na-cc 1.1 180.0 2.0 Using default
> value
> h5-na-cc-nd 1.1 180.0 2.0 Using default
> value
> ca-ca-ca-nd 1.1 180.0 2.0 Using default
> value
> ca-nb-ca-nh 1.1 180.0 2.0 Using default
> value
> ca-hn-nh-hn 1.1 180.0 2.0 Using default
> value
> h5-nb-ca-nb 1.1 180.0 2.0 Using default
> value
> ca-na-ca-nb 1.1 180.0 2.0 Using default
> value
>
> NONBON
>
> The pdb file "X-hclean.pdb" is attached. The portion encoding for SAH is
> as follows:
>
> HETATM 4193 N SAH 266 1.502 -2.774 -2.109 1.00 15.86
> N
> HETATM 4194 CA SAH 266 2.813 -3.459 -2.517 1.00 15.86
> C
> HETATM 4195 CB SAH 266 2.967 -3.475 -4.066 1.00 15.86
> C
> HETATM 4196 CG SAH 266 3.245 -2.124 -4.758 1.00 15.86
> C
> HETATM 4197 SD SAH 266 3.738 -2.253 -6.505 1.00 15.86
> S
> HETATM 4198 C SAH 266 3.980 -2.781 -1.754 1.00 15.86
> C
> HETATM 4199 O SAH 266 3.779 -1.802 -0.998 1.00 15.86
> O
> HETATM 4200 OXT SAH 266 5.110 -3.273 -1.943 1.00 15.86
> O
> HETATM 4201 C5' SAH 266 2.232 -1.756 -7.391 1.00 15.86
> C
> HETATM 4202 C4' SAH 266 1.032 -2.680 -7.153 1.00 15.86
> C
> HETATM 4203 O4' SAH 266 -0.104 -2.118 -7.800 1.00 15.86
> O
> HETATM 4204 C3' SAH 266 1.197 -4.075 -7.780 1.00 15.86
> C
> HETATM 4205 O3' SAH 266 0.904 -5.096 -6.853 1.00 15.86
> O
> HETATM 4206 C2' SAH 266 0.302 -4.047 -9.018 1.00 15.86
> C
> HETATM 4207 O2' SAH 266 -0.262 -5.278 -9.442 1.00 15.86
> O
> HETATM 4208 C1' SAH 266 -0.773 -3.087 -8.539 1.00 15.86
> C
> HETATM 4209 N9 SAH 266 -1.647 -2.446 -9.594 1.00 15.86
> N
> HETATM 4210 C8 SAH 266 -1.348 -2.089 -10.860 1.00 15.86
> C
> HETATM 4211 N7 SAH 266 -2.350 -1.548 -11.508 1.00 15.86
> N
> HETATM 4212 C5 SAH 266 -3.347 -1.523 -10.609 1.00 15.86
> C
> HETATM 4213 C6 SAH 266 -4.680 -1.064 -10.697 1.00 15.86
> C
> HETATM 4214 N6 SAH 266 -5.223 -0.531 -11.864 1.00 15.86
> N
> HETATM 4215 N1 SAH 266 -5.469 -1.165 -9.594 1.00 15.86
> N
> HETATM 4216 C2 SAH 266 -4.943 -1.711 -8.489 1.00 15.86
> C
> HETATM 4217 N3 SAH 266 -3.708 -2.192 -8.289 1.00 15.86
> N
> HETATM 4218 C4 SAH 266 -2.943 -2.064 -9.401 1.00 15.86
> C
> HETATM 4219 H1 SAH 266 0.725 -3.183 -2.611 1.00 0.00
> H
> HETATM 4220 H2 SAH 266 1.343 -2.890 -1.118 1.00 0.00
> H
> HETATM 4221 H3 SAH 266 1.538 -1.787 -2.326 1.00 0.00
> H
> HETATM 4222 HA SAH 266 2.682 -4.361 -2.184 1.00 15.86
> H
> HETATM 4223 HB1 SAH 266 2.174 -3.870 -4.460 1.00 15.86
> H
> HETATM 4224 HB2 SAH 266 3.694 -4.076 -4.292 1.00 15.86
> H
> HETATM 4225 HG1 SAH 266 3.986 -1.678 -4.319 1.00 15.86
> H
> HETATM 4226 HG2 SAH 266 2.483 -1.531 -4.663 1.00 15.86
> H
> HETATM 4227 H5'1 SAH 266 2.443 -1.720 -8.337 1.00 15.86
> H
> HETATM 4228 H5'2 SAH 266 2.012 -0.851 -7.121 1.00 15.86
> H
> HETATM 4229 H4' SAH 266 0.835 -2.716 -6.204 1.00 15.86
> H
> HETATM 4230 H3' SAH 266 2.111 -4.222 -8.069 1.00 15.86
> H
> HETATM 4231 HO3' SAH 266 0.109 -5.016 -6.594 1.00 15.86
> H
> HETATM 4232 H2' SAH 266 0.781 -3.615 -9.743 1.00 15.86
> H
> HETATM 4233 HO2' SAH 266 -0.601 -5.666 -8.778 1.00 15.86
> H
> HETATM 4234 H1' SAH 266 -1.374 -3.545 -7.930 1.00 15.86
> H
> HETATM 4235 H8 SAH 266 -0.462 -2.242 -11.225 1.00 15.86
> H
> HETATM 4236 H61 SAH 266 -6.217 -0.350 -11.914 1.00 0.00
> H
> HETATM 4237 H62 SAH 266 -4.648 -0.496 -12.693 1.00 0.00
> H
> HETATM 4238 H2 SAH 266 -5.543 -1.783 -7.731 1.00 15.86
> H
> END
> --
> Best regards,
>
> JoAnne Babula, Ph.D.
> Research Scientist
> Ridgeline Therapeutics
> 2450 Holcombe Blvd, Suite J
> Houston, TX 77021
>
--
Best regards,
JoAnne Babula, Ph.D.
Research Scientist
Ridgeline Therapeutics
2450 Holcombe Blvd, Suite J
Houston, TX 77021
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Received on Wed Jul 22 2020 - 14:00:04 PDT
