As Amy and I said before, running well does not mean it is correct. Please
read that section of the manual. If you did not make those changes, the
results of your simulations will be wrong.
On Sun, Jun 9, 2024, 3:02 PM Kavinda Kashi Juliyan Gunasinghe via AMBER <
amber.ambermd.org> wrote:
> Hi Amy,
>
> Thank you so much for your suggestions and recommendations. I did use the
> OPC water model coupled with ff19SB forcefield which seem to run well,
> further more I edited the pdb file and minimised further to make sure the
> errors are resolved and to adjust clashes.
>
> Thank you so much,
> Sincerely,
> Jul
>
> Sent from Outlook for Android<https://aka.ms/AAb9ysg>
> ________________________________
> From: He, Amy <he.1768.buckeyemail.osu.edu>
> Sent: Sunday, June 9, 2024 10:06:36 PM
> To: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>;
> AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Parameterization Issue
>
>
> Hi Jul!
>
>
>
> As Dr. Simmerling suggested, it might be helpful to take a quick look at
> “Instructions for implementing ff19SB for a new amino acid (residue)” in a
> recent Amber manual. Because of the XC atom type and CMAP for backbone
> dihedrals new in ff19SB, to apply the latter you might need to check the
> dihedral terms and/or load the frcmod files in a specific order.
>
>
>
> I took a quick look at the commands and leap output too. Some other things
> I was a bit unsure about:
>
> 1- I’m not entirely sure if the charge method (AM1-BCC) works well with
> ff19SB. (For simple chemical groups the difference may be negligible?) The
> ff19SB paper uses RESP fitting for charge derivation.
>
> 2- Based on the log, you haven’t yet solvated the system. But if you’re
> planning to, it’s recommended to use OPC water model instead of TIP3P for
> ff19SB.
>
>
>
> There isn’t a guarding mechanism for not following the recommendations. If
> you don’t, you should still be able to pass the leap step and run
> calculations. These small things have more to do with the quality of the
> prepared parameters. They may or may not be important for your work
> depending on what you want to use the prepare parameters for :>
>
>
>
> Hope this helps!
>
>
>
>
>
> --
>
> Amy He
>
> Forli Lab . TSRI
>
> yihe.scripps.edu
>
>
>
>
>
> From: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>
> Date: Sunday, June 9, 2024 at 7:07 AM
> To: Carlos Simmerling <carlos.simmerling.gmail.com>, AMBER Mailing List <
> amber.ambermd.org>
> Cc: He, Amy <he.1768.buckeyemail.osu.edu>
> Subject: Re: [AMBER] Parameterization Issue
>
> Hi Carlos, Thank you so much for your help. I was able to successfully
> parameterize the non standard residues based after I used parm19. dat. And
> also there were a few errors in the standard residue atom types which I
> resolved manually. Sincerely,
>
> Hi Carlos,
>
>
>
> Thank you so much for your help. I was able to successfully parameterize
> the non standard residues based after I used parm19.dat. And also there
> were a few errors in the standard residue atom types which I resolved
> manually.
>
>
>
> Sincerely,
>
> Jul
>
> ________________________________
>
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Sunday, June 9, 2024 7:33 PM
> To: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>;
> AMBER Mailing List <amber.ambermd.org>
> Cc: He, Amy <he.1768.buckeyemail.osu.edu>
> Subject: Re: [AMBER] Parameterization Issue
>
>
>
> Do you mean that you changed the atom names? They do seem non standard,
> not sure where you got the pdb file. It may have other issues as well,
> check it carefully. Also read thr ff19sb paper or amber manual, non
> standard residues require some extra work beyond just having leap not fail.
>
>
>
>
>
> On Sun, Jun 9, 2024, 9:57 AM Kavinda Kashi Juliyan Gunasinghe via AMBER <
> amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
>
> Hi Amy,
>
> I manually changed the atom IDs and it worked.
>
> Thank you so much,
>
> Sincerely,
> Jul
>
> Sent from Outlook for Android<https://aka.ms/AAb9ysg<
> https://urldefense.com/v3/__https:/aka.ms/AAb9ysg__;!!KGKeukY!zJcM1h8w-GpegWovn_0s65cKNYKnPgLNnTTlWYFzEtWn0GPIRlvlPzY8cTMfpxlMebFNfY5vLEwZoSWeiOlqjWxp0CETV8mzR_0bRD2TVPo$
> >>
> ________________________________
> From: He, Amy <he.1768.buckeyemail.osu.edu<mailto:
> he.1768.buckeyemail.osu.edu>>
> Sent: Sunday, June 9, 2024 1:50:03 PM
> To: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my
> <mailto:kkgunasinghe.swinburne.edu.my>>; AMBER Mailing List <
> amber.ambermd.org<mailto:amber.ambermd.org>>
> Subject: Re: Parameterization Issue
>
>
> Hi Jul,
>
>
>
> Do you have atom types in ff19SB (for example, XC)? If so, you need to
> point parmchk2 to parm19.dat (unlike the tutorial which used parm10.dat).
>
>
>
> I don’t quite get the CHARMGUI part. Can you explain a bit more what
> commands you used and how you got the errors? Since the structure file
> (PDB) does not specify atom types, it shouldn’t matter how you edited the
> structure.
>
>
>
> From: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my
> <mailto:kkgunasinghe.swinburne.edu.my>>
> Date: Sunday, June 9, 2024 at 1:08 AM
> To: He, Amy <he.1768.buckeyemail.osu.edu<mailto:
> he.1768.buckeyemail.osu.edu>>, AMBER Mailing List <amber.ambermd.org
> <mailto:amber.ambermd.org>>
> Subject: Re: Parameterization Issue
>
> Hi Amy, I tried and it gave me these errors. Error: Could not find bond
> parameter for: C - NT Error: Could not find bond parameter for: C - NT
> Error: Could not find bond parameter for: C - NT Error: Could not find bond
> parameter for: C - NT
>
> Hi Amy,
>
>
>
> I tried and it gave me these errors.
>
>
>
> Error: Could not find bond parameter for: C - NT
>
>
>
> Error: Could not find bond parameter for: C - NT
>
>
>
> Error: Could not find bond parameter for: C - NT
>
>
>
> Error: Could not find bond parameter for: C - NT
>
>
>
> Error: Could not find bond parameter for: C - NT
>
>
>
> Error: Could not find bond parameter for: C - NT
>
>
>
> Error: Could not find bond parameter for: C - NT
>
>
>
> Error: Could not find bond parameter for: C - NT
>
> Checking for angle parameters.
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
>
>
> Error: Could not find angle parameter: O - C - NT
>
>
>
> Error: Could not find angle parameter: C - NT - H
>
>
>
> Error: Could not find angle parameter: C - NT - CT
>
>
>
> Error: Could not find angle parameter: XC - C - NT
>
> However, I know that for using the CIF file for CGU from protein databank
> the main chain file should be this with a charge of -2
>
> >HEAD_NAME N
>
> TAIL_NAME C
>
> MAIN_CHAIN CA
>
> OMIT_NAME H2
>
> OMIT_NAME OXT
>
> OMIT_NAME HXT
>
> OMIT_NAME HE12
>
> OMIT_NAME HE22
>
> PRE_HEAD_TYPE C
>
> POST_TAIL_TYPE N
>
> CHARGE -2.0
>
>
>
> However, in my protein structure where I modified the CGU using CHARMM-GUI
> the atom types seem to be different. In this case what should I do? I have
> attached my PDB structure file in this email.
>
>
>
> Thank you so much,
>
> Jul
>
> ________________________________
>
> From: He, Amy <he.1768.buckeyemail.osu.edu<mailto:
> he.1768.buckeyemail.osu.edu>>
> Sent: Sunday, June 9, 2024 1:14 PM
> To: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my
> <mailto:kkgunasinghe.swinburne.edu.my>>; AMBER Mailing List <
> amber.ambermd.org<mailto:amber.ambermd.org>>
> Subject: Re: Parameterization Issue
>
>
>
> Hi Jul,
>
>
>
> Instead of making one, you could download a component cif file from the
> corresponding PDB entry for CGU:
>
> https://www.rcsb.org/ligand/CGU<
> https://urldefense.com/v3/__https:/www.rcsb.org/ligand/CGU__;!!KGKeukY!zJcM1h8w-GpegWovn_0s65cKNYKnPgLNnTTlWYFzEtWn0GPIRlvlPzY8cTMfpxlMebFNfY5vLEwZoSWeiOlqjWxp0CETV8mzR_0bBVAJpYs$
> ><
> https://urldefense.com/v3/__https:/www.rcsb.org/ligand/CGU__;!!KGKeukY!x1PFesa2AwmFlE6sF3MMV6EyxzdQMsR0IpMfC58_97M0ENwdtev-raZugT2FZPgj5wGTGC0hMLjBHhY9ImLa9lWyCqFqC1JIaEZT2HSm3g4$
> >
>
>
>
> If your residue is embedded (linking two other residues through the
> backbone), you might have to make your own mainchain file. Tutorial 5
> Section 3 does a great demonstration for that:
>
> https://ambermd.org/tutorials/basic/tutorial5/index.php<
> https://urldefense.com/v3/__https:/ambermd.org/tutorials/basic/tutorial5/index.php__;!!KGKeukY!zJcM1h8w-GpegWovn_0s65cKNYKnPgLNnTTlWYFzEtWn0GPIRlvlPzY8cTMfpxlMebFNfY5vLEwZoSWeiOlqjWxp0CETV8mzR_0brEYGXxE$
> ><
> https://urldefense.com/v3/__https:/ambermd.org/tutorials/basic/tutorial5/index.php__;!!KGKeukY!x1PFesa2AwmFlE6sF3MMV6EyxzdQMsR0IpMfC58_97M0ENwdtev-raZugT2FZPgj5wGTGC0hMLjBHhY9ImLa9lWyCqFqC1JIaEZTFVSSfyU$
> >
>
>
>
> If you need to modify the protonation state, you could edit the
> composition and specify the total charge of the residue to your liking,
> also in the mainchain file.
>
>
>
> From: Kavinda Kashi Juliyan Gunasinghe via AMBER <amber.ambermd.org
> <mailto:amber.ambermd.org>>
> Date: Saturday, June 8, 2024 at 10:19 PM
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
> Subject: [AMBER] Parameterization Issue
>
>
> Dear AMBER users,
>
> I have modelled an AF3 protein strucutre which consists of
> Gamma-carboxylated Glus (CGU). However, I have an issue with generating the
> Main Chain file for the which gives me several errors that in which several
> bond and angle parameters are missing. Can I know how I can generate the
> correct CIF file and then generate the correct main chain file for this
> protein? I have attached my protein structure in this email.
>
> Thank you inadvance!
> Jul
>
>
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Received on Mon Jun 10 2024 - 03:30:02 PDT
