Thank you so much, Prof. Simmering. That works perfectly. By the way, there was no error when I tried it with ff19SB. Can we consider the TYD parameters under ff19SB to be reliable?
Best,
Xiangwei
From: Carlos Simmerling <carlos.simmerling.stonybrook.edu>
Sent: Wednesday, November 8, 2023 8:55 AM
To: Xiangwei Zhu <xzhu.sutrobio.com>
Cc: Carlos Simmerling <carlos.simmerling.stonybrook.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Model a protein with Tyrosine anion
sorry for the delay. You can download the files here: https://github.com/csimmerling/modified-AA-params
On Mon, Nov 6, 2023 at 3:48 PM Xiangwei Zhu <xzhu.sutrobio.com<mailto:xzhu.sutrobio.com>> wrote:
Hi Prof. Simmerling,
Could you please send me the TYD parameters? Thanks a lot.
Xiangwei
From: Carlos Simmerling <carlos.simmerling.stonybrook.edu<mailto:carlos.simmerling.stonybrook.edu>>
Sent: Friday, November 3, 2023 4:39 AM
To: Xiangwei Zhu <xzhu.sutrobio.com<mailto:xzhu.sutrobio.com>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] Model a protein with Tyrosine anion
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<mailto: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<mailto:todd.minehardt.gmail.com>>
Sent: Thursday, November 2, 2023 3:11 PM
To: Xiangwei Zhu <xzhu.sutrobio.com<mailto:xzhu.sutrobio.com>>; AMBER Mailing List <amber.ambermd.org<mailto: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><
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><
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><mailto: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 Wed Nov 08 2023 - 14:30:02 PST
