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-- 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$> If you need to modify the protonation state, you could edit the composition and specify the total charge of the residue to your liking, also in the mainchain file. From: Kavinda Kashi Juliyan Gunasinghe via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> Date: Saturday, June 8, 2024 at 10:19 PM To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>> Subject: [AMBER] Parameterization Issue Dear AMBER users, I have modelled an AF3 protein strucutre which consists of Gamma-carboxylated Glus (CGU). However, I have an issue with generating the Main Chain file for the which gives me several errors that in which several bond and angle parameters are missing. Can I know how I can generate the correct CIF file and then generate the correct main chain file for this protein? I have attached my protein structure in this email. Thank you inadvance! Jul [NOTICE] This e-mail and any attachments are confidential and intended only for the use of the addressee. They may contain information that is privileged or protected by copyright. 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Please consider the environment before printing this email. _______________________________________________ AMBER mailing list AMBER.ambermd.org<mailto:AMBER.ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!zJcM1h8w-GpegWovn_0s65cKNYKnPgLNnTTlWYFzEtWn0GPIRlvlPzY8cTMfpxlMebFNfY5vLEwZoSWeiOlqjWxp0CETV8mzR_0bz0UH-6w$> _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Jun 09 2024 - 10:00:02 PDT