Changing the atom type worked. Thank you so much, Amy.
Best,
Noureen
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Tuesday, July 30, 2024 1:39 AM
To: Abdelrahman, Noureen <noureen.unc.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Atom type of DU does not exist in PARMCHK.DAT
Hi Noureen,
In the prepin file, atom NC didn’t get a valid atom type. This is because in the previous step, you specified ff19SB atom types (by the -at option) to generate the ac file.
A quick, dirty fix is to just modify the atom types in the prepin file. You can take a look at available atom types in parm19.dat and choose an existing type. The best guess might be NB or N*, both considered “same as (gaff2 atom type) nc”. Once you’re able to generate the frcmod files, you will see that either way, parmchk2 will find the exact same parameters from gaff2 to fill in the missing bond, angles and torsions. Because parm19.dat can’t directly provide these parameters for the nitrogens – in this sense, parm19.dat isn’t really helpful as the source of parameters for 9UY.
The tedious solution is to type the residue in gaff2. If you do this, you will see that the atm type for atom NC is:
ne 14.01 0.530 Inner Sp2 N in conjugated systems
For atom NB it’s:
nc 14.01 0.530 Sp2 N in non-pure aromatic systems
nd 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc
Previously, to use this kind of gaff2 prepin files, I looked up and wrote some additional parameters to the frcmod file. These include the bond, angle and torsion parameters at the interface of gaff2/ff19SB system that are typed in a hybrid manner. It’s possible, but takes more work to set up the system :<
Hope this is mildly helpful!
--
Amy He
Forli Lab . TSRI
yihe.scripps.edu
From: Abdelrahman, Noureen via AMBER <amber.ambermd.org>
Date: Monday, July 29, 2024 at 1:32 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Atom type of DU does not exist in PARMCHK.DAT
I have also attached the pdb file of the protein that I want to simulate.
________________________________
From: Abdelrahman, Noureen
Sent: Monday, July 29, 2024 1:49 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Atom type of DU does not exist in PARMCHK.DAT
Hello,
I am using Amber tutorial Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue<
https://urldefense.com/v3/__https://ambermd.org/tutorials/basic/tutorial5/__;!!KGKeukY!yqeII2BO2kU9rEBltwQBxP8LnQwE1ihUSaZFOXCgdKBN3xGScmXwmfCZSfwK1K-AhmwpSC_3a8uoz_91ESbs-4M-BZo$ > <
https://urldefense.com/v3/__https://ambermd.org/tutorials/basic/tutorial5/__;!!KGKeukY!yqeII2BO2kU9rEBltwQBxP8LnQwE1ihUSaZFOXCgdKBN3xGScmXwmfCZSfwK1K-AhmwpSC_3a8uoz_91ESbs-4M-BZo$ > to simulate a protein that has a nonstandard amino acid residue using tleap. The problem is that when I run the following command, I get an error message.
Command:
parmchk2 -i 9UY.prepin -f prepi -o frcmod.9UY -a Y \ -p $AMBERHOME/dat/leap/parm/parm19.dat
Error message:
Atom type of DU does not exist in PARMCHK.DAT
Attached are my .cif and .mc files that I used to get the prepin file (also attached). Does anyone know why I am receiving that error? I have used this tutorial before with a different protein, and it ran smoothly. So, I think there might be an issue with my .mc file or the .cif file on pdb.
Thanks,
Noureen
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Received on Thu Aug 01 2024 - 13:00:01 PDT
