we have pre-built TYD parameters and library files for ff14SB that I can
send later today.
On Thu, Nov 2, 2023 at 11:18 PM Xiangwei Zhu via AMBER <amber.ambermd.org>
wrote:
> Thanks for the detailed instructions, Todd. I can reproduce them and
> generate the exact same TYD.prepi and TYD.frcmod. But I got errors when
> trying steps 5 through 8 on my own pdb file. Errors were mostly related to
> the missing of bond, angle, and torsion parameters between atoms from TYD
> and its neighbor residues. Not sure what was missed. Below is an example
> pdb file. Could you please give it a try? Thanks,
>
> Xiangwei
>
> test.pdb
>
> --------------------------------------------------------------------------------
> ATOM 1 H1 ACE 1 9.555 -90.040 -55.409 1.00 0.00
> ATOM 2 CH3 ACE 1 9.163 -91.057 -55.409 1.00 0.00
> ATOM 3 H2 ACE 1 9.511 -91.581 -54.519 1.00 0.00
> ATOM 4 H3 ACE 1 9.511 -91.581 -56.299 1.00 0.00
> ATOM 5 C ACE 1 7.633 -91.057 -55.409 1.00 0.00
> ATOM 6 O ACE 1 7.009 -89.998 -55.409 1.00 0.00
> ATOM 7 N VAL 2 8.685 -91.044 -54.603 1.00 0.00
> ATOM 8 H VAL 2 9.629 -90.978 -54.955 1.00 0.00
> ATOM 9 CA VAL 2 8.494 -91.237 -53.173 1.00 0.00
> ATOM 10 HA VAL 2 7.432 -91.250 -52.939 1.00 0.00
> ATOM 11 CB VAL 2 9.048 -92.578 -52.653 1.00 0.00
> ATOM 12 HB VAL 2 10.103 -92.620 -52.699 1.00 0.00
> ATOM 13 CG1 VAL 2 8.890 -92.661 -51.144 1.00 0.00
> ATOM 14 HG11 VAL 2 9.159 -93.660 -50.798 1.00 0.00
> ATOM 15 HG12 VAL 2 9.541 -91.948 -50.636 1.00 0.00
> ATOM 16 HG13 VAL 2 7.851 -92.460 -50.881 1.00 0.00
> ATOM 17 CG2 VAL 2 8.342 -93.746 -53.324 1.00 0.00
> ATOM 18 HG21 VAL 2 8.546 -93.745 -54.395 1.00 0.00
> ATOM 19 HG22 VAL 2 8.706 -94.687 -52.910 1.00 0.00
> ATOM 20 HG23 VAL 2 7.265 -93.677 -53.164 1.00 0.00
> ATOM 21 C VAL 2 9.087 -90.084 -52.385 1.00 0.00
> ATOM 22 O VAL 2 10.280 -89.810 -52.465 1.00 0.00
> ATOM 23 N TYD 3 8.230 -89.400 -51.637 1.00 0.00
> ATOM 24 H TYD 3 7.256 -89.665 -51.618 1.00 0.00
> ATOM 25 CA TYD 3 8.658 -88.287 -50.811 1.00 0.00
> ATOM 26 HA TYD 3 9.629 -87.912 -51.138 1.00 0.00
> ATOM 27 CB TYD 3 7.653 -87.143 -50.912 1.00 0.00
> ATOM 28 HB2 TYD 3 6.640 -87.531 -50.786 1.00 0.00
> ATOM 29 HB3 TYD 3 7.838 -86.443 -50.096 1.00 0.00
> ATOM 30 CG TYD 3 7.737 -86.385 -52.220 1.00 0.00
> ATOM 31 CD1 TYD 3 7.471 -87.036 -53.437 1.00 0.00
> ATOM 32 HD1 TYD 3 7.116 -88.054 -53.458 1.00 0.00
> ATOM 33 CE1 TYD 3 7.626 -86.356 -54.649 1.00 0.00
> ATOM 34 HE1 TYD 3 7.408 -86.843 -55.581 1.00 0.00
> ATOM 35 CZ TYD 3 8.074 -85.029 -54.653 1.00 0.00
> ATOM 36 OH TYD 3 8.301 -84.438 -55.844 1.00 0.00
> ATOM 38 CE2 TYD 3 8.305 -84.351 -53.441 1.00 0.00
> ATOM 39 HE2 TYD 3 8.628 -83.325 -53.458 1.00 0.00
> ATOM 40 CD2 TYD 3 8.135 -85.035 -52.221 1.00 0.00
> ATOM 41 HD2 TYD 3 8.340 -84.539 -51.286 1.00 0.00
> ATOM 42 C TYD 3 8.757 -88.702 -49.364 1.00 0.00
> ATOM 43 O TYD 3 8.005 -89.556 -48.894 1.00 0.00
> ATOM 44 N SER 4 9.675 -88.075 -48.649 1.00 0.00
> ATOM 45 H SER 4 10.274 -87.385 -49.078 1.00 0.00
> ATOM 46 CA SER 4 9.734 -88.242 -47.215 1.00 0.00
> ATOM 47 HA SER 4 8.799 -88.662 -46.842 1.00 0.00
> ATOM 48 CB SER 4 10.872 -89.179 -46.813 1.00 0.00
> ATOM 49 HB2 SER 4 10.664 -89.585 -45.822 1.00 0.00
> ATOM 50 HB3 SER 4 10.943 -90.005 -47.522 1.00 0.00
> ATOM 51 OG SER 4 12.097 -88.479 -46.758 1.00 0.00
> ATOM 52 HG SER 4 12.758 -89.008 -47.219 1.00 0.00
> ATOM 53 C SER 4 9.921 -86.870 -46.586 1.00 0.00
> ATOM 54 O SER 4 10.463 -85.956 -47.209 1.00 0.00
> ATOM 55 N NME 5 9.454 -86.732 -45.354 1.00 0.00
> ATOM 56 H NME 5 9.007 -87.512 -44.893 1.00 0.00
> ATOM 57 C NME 5 9.562 -85.482 -44.630 1.00 0.00
> ATOM 58 H1 NME 5 10.063 -84.742 -45.254 1.00 0.00
> ATOM 59 H2 NME 5 8.565 -85.123 -44.372 1.00 0.00
> ATOM 60 H3 NME 5 10.138 -85.638 -43.718 1.00 0.00
> TER
> END
>
> ----------------------------------------------------------------------------------------
>
> From: Todd Minehardt <todd.minehardt.gmail.com>
> Sent: Thursday, November 2, 2023 3:11 PM
> To: Xiangwei Zhu <xzhu.sutrobio.com>; AMBER Mailing List <
> amber.ambermd.org>
> Subject: Re: [AMBER] Model a protein with Tyrosine anion
>
> 1. Save your PDB file as TYD.pdb (I'm making up the name TYrosine
> Deprotonated), and I am assuming you want the hydrogen on the OH in the
> ring removed;
> 2. Remove the line with the atom type 'HH" (line 15 in your file, above);
>
> It will look like:
>
> ATOM 3371 N TYD 214 1.720 -90.946 -37.554 -0.41 0.00
> N
> ATOM 3372 H TYD 214 1.540 -90.149 -38.148 0.27 0.00
> H
> ATOM 3373 CA TYD 214 3.000 -91.015 -36.877 -0.00 0.00
> C
> ATOM 3374 HA TYD 214 3.441 -92.000 -37.040 0.08 0.00
> H
> ATOM 3375 CB TYD 214 3.946 -89.962 -37.446 -0.01 0.00
> C
> ATOM 3376 HB2 TYD 214 4.088 -90.161 -38.509 0.02 0.00
> H
> ATOM 3377 HB3 TYD 214 3.508 -88.971 -37.358 0.02 0.00
> H
> ATOM 3378 CG TYD 214 5.285 -89.953 -36.769 -0.00 0.00
> C
> ATOM 3379 CD1 TYD 214 5.506 -89.174 -35.638 -0.19 0.00
> C
> ATOM 3380 HD1 TYD 214 4.709 -88.560 -35.242 0.16 0.00
> H
> ATOM 3381 CE1 TYD 214 6.726 -89.173 -35.006 -0.23 0.00
> C
> ATOM 3382 HE1 TYD 214 6.883 -88.567 -34.126 0.16 0.00
> H
> ATOM 3383 CZ TYD 214 7.751 -89.956 -35.506 0.32 0.00
> C
> ATOM 3384 OH TYD 214 8.969 -89.949 -34.874 -0.55 0.00
> O
> ATOM 3386 CE2 TYD 214 7.562 -90.739 -36.631 -0.23 0.00
> C
> ATOM 3387 HE2 TYD 214 8.366 -91.353 -37.013 0.16 0.00
> H
> ATOM 3388 CD2 TYD 214 6.331 -90.736 -37.253 -0.19 0.00
> C
> ATOM 3389 HD2 TYD 214 6.182 -91.356 -38.124 0.16 0.00
> H
> ATOM 3390 C TYD 214 2.814 -90.809 -35.372 0.59 0.00
> C
> ATOM 3391 O TYD 214 3.416 -91.509 -34.552 -0.56 0.00
> O
>
> 3. Create the prepi file:
> antechamber -fi pdb -i TYD.pdb -fo prepi -o TYD.prepi -seq y -rn TYD -nc
> -1 -c bcc -j 5
>
> 4. Create the frcmod file:
> parmchk2 -i TYD.prepi -f prepi -o TYD.frcmod
>
> 5. Copy your file TYD.pdb to test.pdb and remove several of the atoms
> randomly (say, 10 of them);
>
> It will look like:
>
> ATOM 3371 N TYD 214 1.720 -90.946 -37.554 -0.41 0.00
> N
> ATOM 3373 CA TYD 214 3.000 -91.015 -36.877 -0.00 0.00
> C
> ATOM 3375 CB TYD 214 3.946 -89.962 -37.446 -0.01 0.00
> C
> ATOM 3378 CG TYD 214 5.285 -89.953 -36.769 -0.00 0.00
> C
> ATOM 3379 CD1 TYD 214 5.506 -89.174 -35.638 -0.19 0.00
> C
> ATOM 3381 CE1 TYD 214 6.726 -89.173 -35.006 -0.23 0.00
> C
> ATOM 3386 CE2 TYD 214 7.562 -90.739 -36.631 -0.23 0.00
> C
> ATOM 3387 HE2 TYD 214 8.366 -91.353 -37.013 0.16 0.00
> H
> ATOM 3388 CD2 TYD 214 6.331 -90.736 -37.253 -0.19 0.00
> C
> ATOM 3389 HD2 TYD 214 6.182 -91.356 -38.124 0.16 0.00
> H
> ATOM 3390 C TYD 214 2.814 -90.809 -35.372 0.59 0.00
> C
> ATOM 3391 O TYD 214 3.416 -91.509 -34.552 -0.56 0.00
> O
> 6. Using vi - and only vi - create a file called tleap.in<http://tleap.in>,
> in which you will have:
>
> source leaprc.protein.ff19SB
> source leaprc.gaff
> loadamberprep TYD.prepi
> loadamberparams TYD.frcmod
> mol = loadpdb test.pdb
> saveamberparm mol TYD.prmtop TYD.crd
>
> 7. tleap -s -f tleap.in<http://tleap.in>
>
> 8. We are doing steps 5 through 8 to make sure the prepi and frcmod files
> recreate the desired molecole (tyrosine minus the -OH group hydrogen):
>
> ambpdb -p TYD.prmtop -c TYD.crd > test_check.pdb
> 9. Look at test_check.pdb in a viewer (Chimerax, pymol, Avogodro2, etc.)
> and make sure it looks ok.
>
> 10. In your system of interest, you will replace each occurrence of the
> new tyrosine with the symbol TYD and load the parameters as in step 6.
>
> 11. You are still not off the hook, since the process doesn't always
> produce the correct atom types (like aromatic carbons), so you might need
> to manually go into the prepi file and change things to reflect the proper
> chemistry.
>
> 12. In case you want to cut straight to the chase - and I have not checked
> that the prepi file is correct (but hey, it does produce the thing you
> want):
>
> TYD.prepi:
>
>
> -----------------------------------------------------------------------------------------------------------
> 0 0 2
>
> This is a remark line
> molecule.res
> TYD INT 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 1.523 111.21 .0 .00000
> 4 O o M 3 2 1 1.540 111.208 -180.000 -0.459000
> 5 C c1 M 4 3 2 1.235 60.822 130.486 -0.023000
> 6 CA c3 M 5 4 3 1.530 121.164 -120.024 -0.047000
> 7 N n2 S 6 5 4 1.450 110.215 137.156 -0.272000
> 8 H hn E 7 6 5 1.010 118.002 110.354 0.116000
> 9 HA h1 E 6 5 4 1.091 108.509 17.547 0.147000
> 10 CB c3 M 6 5 4 1.526 110.441 -101.213 -0.118000
> 11 HB2 hc E 10 6 5 1.091 108.559 177.756 0.079500
> 12 HB3 hc E 10 6 5 1.087 110.438 -64.844 0.079500
> 13 CG ca M 10 6 5 1.500 112.906 56.850 -0.212000
> 14 CD1 ca M 13 10 6 1.391 120.798 -88.734 -0.084000
> 15 HD1 ha E 14 13 10 1.081 119.915 -0.460 0.096500
> 16 CE1 ca M 14 13 10 1.374 121.030 179.305 -0.244000
> 17 HE1 ha E 16 14 13 1.080 120.285 -179.719 0.142500
> 18 CZ ca M 16 14 13 1.383 119.422 0.218 0.226000
> 19 OH o E 18 16 14 1.372 119.230 179.810 -0.342000
> 20 CE2 ca M 18 16 14 1.384 120.862 -0.072 -0.244000
> 21 HE2 ha E 20 18 16 1.081 120.463 -179.646 0.142500
> 22 CD2 ca M 20 18 16 1.379 119.168 -0.215 -0.084000
> 23 HD2 ha E 22 20 18 1.079 119.067 -179.316 0.096500
>
>
> LOOP
> CD2 CG
>
> IMPROPER
> CB CD1 CG CD2
> CG CE1 CD1 HD1
> CD1 CZ CE1 HE1
> CE1 CE2 CZ OH
> CZ CD2 CE2 HE2
> CG CE2 CD2 HD2
>
> DONE
> STOP
>
>
> -----------------------------------------------------------------------------------------------------------
>
> TYD.frcmod:
>
>
> -----------------------------------------------------------------------------------------------------------
> Remark line goes here
> MASS
>
> BOND
>
> ANGLE
> c3-c1-o 57.930 180.000 Calculated with empirical approach for
> c3-c1-o
> c1-c3-n2 68.008 109.895 Calculated with empirical approach for
> c1-c3-n2
>
> DIHE
>
> IMPROPER
> ca-ca-ca-ha 1.1 180.0 2.0 Using general
> improper torsional angle X- X-ca-ha, penalty score= 6.0)
> ca-ca-ca-o 1.1 180.0 2.0 Using the
> default value
>
> NONBON
>
> -----------------------------------------------------------------------------------------------------------
>
> Cheers,
>
> Todd
>
> On Thu, Nov 2, 2023 at 3:35 PM Xiangwei Zhu via AMBER <amber.ambermd.org
> <mailto:amber.ambermd.org>> wrote:
> Hi All,
> I'm working on a protein that needs to have one of its tyrosine
> deprotonated. The coordinate is shown below. A few questions on it:
> 1. Is there a best of practice to do the modification in tleap?
> 2. How to change it manually?
> 3. How to load the correct force field for tyrosine anion?
> Thanks a lot!
> Xiangwei
>
> Below is the coordinate:
> --------------------------------
>
> ATOM 3371 N TYR 214 1.720 -90.946 -37.554 -0.41 0.00
> N
> ATOM 3372 H TYR 214 1.540 -90.149 -38.148 0.27 0.00
> H
> ATOM 3373 CA TYR 214 3.000 -91.015 -36.877 -0.00 0.00
> C
> ATOM 3374 HA TYR 214 3.441 -92.000 -37.040 0.08 0.00
> H
> ATOM 3375 CB TYR 214 3.946 -89.962 -37.446 -0.01 0.00
> C
> ATOM 3376 HB2 TYR 214 4.088 -90.161 -38.509 0.02 0.00
> H
> ATOM 3377 HB3 TYR 214 3.508 -88.971 -37.358 0.02 0.00
> H
> ATOM 3378 CG TYR 214 5.285 -89.953 -36.769 -0.00 0.00
> C
> ATOM 3379 CD1 TYR 214 5.506 -89.174 -35.638 -0.19 0.00
> C
> ATOM 3380 HD1 TYR 214 4.709 -88.560 -35.242 0.16 0.00
> H
> ATOM 3381 CE1 TYR 214 6.726 -89.173 -35.006 -0.23 0.00
> C
> ATOM 3382 HE1 TYR 214 6.883 -88.567 -34.126 0.16 0.00
> H
> ATOM 3383 CZ TYR 214 7.751 -89.956 -35.506 0.32 0.00
> C
> ATOM 3384 OH TYR 214 8.969 -89.949 -34.874 -0.55 0.00
> O
> ATOM 3385 HH TYR 214 9.571 -90.629 -35.191 0.39 0.00
> H
> ATOM 3386 CE2 TYR 214 7.562 -90.739 -36.631 -0.23 0.00
> C
> ATOM 3387 HE2 TYR 214 8.366 -91.353 -37.013 0.16 0.00
> H
> ATOM 3388 CD2 TYR 214 6.331 -90.736 -37.253 -0.19 0.00
> C
> ATOM 3389 HD2 TYR 214 6.182 -91.356 -38.124 0.16 0.00
> H
> ATOM 3390 C TYR 214 2.814 -90.809 -35.372 0.59 0.00
> C
> ATOM 3391 O TYR 214 3.416 -91.509 -34.552 -0.56 0.00
> O
>
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Received on Fri Nov 03 2023 - 05:00:03 PDT
