Hi Amy,
To update you I was able to resolve the issue with the CGUs. However, Im encountering a different issue with some standard residues having different atom parameters. When trying to parameterize I get this error:
FATAL: Atom .R<ILE 5>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 9>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 35>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 44>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 58>.A<CD 20> does not have a type.
FATAL: Atom .R<CLYS 103>.A<OT1 24> does not have a type.
FATAL: Atom .R<CLYS 103>.A<OT2 25> does not have a type.
FATAL: Atom .R<ILE 108>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 112>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 138>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 147>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 161>.A<CD 20> does not have a type.
FATAL: Atom .R<CLYS 206>.A<OT1 24> does not have a type.
FATAL: Atom .R<CLYS 206>.A<OT2 25> does not have a type.
How can I resolve this?, can I manually change the atom types?
Sincerely,
Jul
________________________________
From: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>
Sent: Sunday, June 9, 2024 3:01 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Parameterization Issue
Hi Amy,
I used the CHARMM-GUI online server to add the residue mutations to the CGUs. It's a direct GUI based system where you clock and add the mutations to the Glu residues to convert them to CGU and that's about it. You can see that in the PDB I have attached in this email. I have outlined what I did and have provided my input codes and the outputs in this email.
First I downloaded the CIF file from PDB for cgu (attached in the email).
Then I used antechamber using the following comand
>antechamber -fi ccif -i CGU.cif -bk CGU -fo ac -o cgu.ac -c bcc -at amber -nc -2
output: cgu.ac (attached in email).
Next, I used prepgen using following command
>prepgen -i cgu.ac -o cgu.prepin -m cgu.mc -rn CGU
Output: cgu.prepin (attached) and the message provided below.
Output:
PRE_HEAD_TYPE is C
POST_TAIL_TYPE is N
Net charge of truncated molecule is -2.00
HEAD_ATOM 1 N
TAIL_ATOM 3 C
MAIN_CHAIN 1 1 N
MAIN_CHAIN 2 2 CA
MAIN_CHAIN 3 3 C
OMIT_ATOM 1 15 H2
OMIT_ATOM 2 5 OXT
OMIT_ATOM 3 17 HXT
OMIT_ATOM 4 21 HE12
OMIT_ATOM 5 22 HE22
Number of mainchain atoms (including head and tail atom): 3
Number of omited atoms: 5
Info: There is a bond linking a non-head and non-tail residue atom (OE12) and an omitted atom (HE12).
You need to specifically add this bond in LEaP using the command 'bond <atom1> <atom2> [order]'
to link OE12 to an atom in another residue (similar to disulfide bonds)!
Info: There is a bond linking a non-head and non-tail residue atom (OE22) and an omitted atom (HE22).
You need to specifically add this bond in LEaP using the command 'bond <atom1> <atom2> [order]'
to link OE22 to an atom in another residue (similar to disulfide bonds)!
Next, using the prepin file and the cgu.ac files I generated the parameters using parm19.dat;
>parmchk2 -i cgu.prepin -f prepi -o frcmod.cgu -a Y \
-p ~/Desktop/amber20_src/dat/leap/parm/parm19.dat
>grep -v "ATTN" frcmod.cgu > frcmod1.cgu
>parmchk2 -i cgu.prepin -f prepi -o frcmod2.cgu
Then I used tleap where all errors and mistakes are shown in the tleap.log file.
Thank you so much,
Sincerely,
Jul
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Sunday, June 9, 2024 1:50 PM
To: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>; AMBER Mailing List <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>
Date: Sunday, June 9, 2024 at 1:08 AM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <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>
Sent: Sunday, June 9, 2024 1:14 PM
To: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>; AMBER Mailing List <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!x1PFesa2AwmFlE6sF3MMV6EyxzdQMsR0IpMfC58_97M0ENwdtev-raZugT2FZPgj5wGTGC0hMLjBHhY9ImLa9lWyCqFqC1JIaEZT2HSm3g4$>
If your residue is embedded (linking two other residues through the backbone), you might have to make your own mainchain file. Tutorial 5 Section 3 does a great demonstration for that:
https://ambermd.org/tutorials/basic/tutorial5/index.php<
https://urldefense.com/v3/__https:/ambermd.org/tutorials/basic/tutorial5/index.php__;!!KGKeukY!x1PFesa2AwmFlE6sF3MMV6EyxzdQMsR0IpMfC58_97M0ENwdtev-raZugT2FZPgj5wGTGC0hMLjBHhY9ImLa9lWyCqFqC1JIaEZTFVSSfyU$>
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>
Date: Saturday, June 8, 2024 at 10:19 PM
To: AMBER Mailing List <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 Sun Jun 09 2024 - 06:30:02 PDT
