Hello, the structure of molecule was optimized via AM1-BCC or other QM methods?
Maybe you can also add your pdb file as attachment.
> -----原始邮件-----
> 发件人: "Rosa Teijeiro Juiz via AMBER" <amber.ambermd.org>
> 发送时间: 2024-09-10 18:14:48 (星期二)
> 收件人: amber.ambermd.org
> 抄送:
> 主题: [AMBER] atom does not have a type error, ff15ipq
>
> Dear AMBER users,
>
> I am trying to learn how to use ff15ipq in order to simulate proteins
> with unnatural amino acids. My problem is that, while following the
> tutorial (
https://ambermd.org/tutorials/advanced/tutorial36/index.php),
> after modifying the protein with Chimera, when I try to proceed with the
> solvation step with tleap but here the problems start:
>
> First, after trying to load the pdb file with the corrected atom names,
> I got this error:
>
> > GB1 = loadPdb 1pgb-m2.pdb
> Loading PDB file: ./1pgb-m2.pdb
> Created a new atom named: CB within residue: .R<aib 48="">
> Added missing heavy atom: .R<aib 48="">.A<cb1 4="">
>
> Note: Bond: Maximum coordination exceeded on .R<aib 48="">.A<hb1 5="">
>
> Note: -- setting atoms pert=true overrides default limits
> ATOMS NOT BONDED: .R<aib 48="">.A<cb 14=""> .R<aib 48="">.A<hb1 5="">
> !FATAL ERROR----------------------------------------
> !FATAL: In file
> [/opt/amber24_src/AmberTools/src/leap/src/leap/atom.c], line 444
> !FATAL: Message: bondAtomProblem found
> !
>
> !ABORTING.
>
> Then, I saw that for someone, deleting the CONECT lines from the pdb
> file worked to solve this, so I tried that and now, while it does allow
> me to load the pdb file, I get this other fatal error when I try to save
> amber parameters:
>
> > gb1 = loadPdb 1pgb-m22.pdb
> Loading PDB file: ./1pgb-m22.pdb
> Created a new atom named: CB within residue: .R<aib 48="">
> Added missing heavy atom: .R<aib 48="">.A<cb1 4="">
> total atoms in file: 930
> Leap added 1 missing atom according to residue templates:
> 1 Heavy
> The file contained 1 atoms not in residue templates
>
> Warning: Since the number of added atoms equals the number of missing
> atoms, it is likely
> that some atoms had incorrect names; you may want to use addPdbAtomMap
> to map
> these names, or change the names in the PDB file.
>
> > saveAmberParm gb1 gb1_solv.prmtop gb1_solv.inpcrd
> Checking Unit.
>
> Warning: There is a bond of 3.473 angstroms between CB1 and HB1 atoms:
> ------- .R<aib 48="">.A<cb1 4=""> and .R<aib 48="">.A<hb1 5="">
>
> Warning: The unperturbed charge of the unit (-4.000000) is not zero.
> FATAL: Atom .R<aib 48="">.A<cb 14=""> does not have a type.
>
> Error: Failed to generate parameters
>
> Warning: Parameter file was not saved.
>
>
> In one of the warnings it tells me to use addPdbAtomMap, but I also
> don´t really get what it wants me to do, since I already tried changing
> names in the pdb file and that didn't work.
>
> The lines in the pdb file look like this currently ( my problem also is
> that the example for this file on the tutorial is not accessible, and
> therefore I can´t really check if my pdb file is correct or if the
> problem is there):
>
> ATOM 716 N AIB A 48 21.529 11.871 22.356 1.00 22.45
> N
> ATOM 717 CA AIB A 48 22.584 12.858 22.345 1.00 22.79
> C
> ATOM 718 C AIB A 48 22.060 14.258 21.934 1.00 23.33
> C
> ATOM 719 O AIB A 48 22.758 15.267 22.083 1.00 24.83
> O
> ATOM 720 C AIB A 48 23.675 12.428 21.380 1.00 23.59
> C
> ATOM 721 H AIB A 48 21.430 11.268 21.552 1.00 0.00
> H
> ATOM 722 CB2 AIB A 48 23.180 12.951 23.745 1.00 0.00
> C
> ATOM 723 HB1 AIB A 48 24.470 13.174 21.373 1.00 0.00
> H
> ATOM 724 HB2 AIB A 48 24.081 11.467 21.696 1.00 0.00
> H
> ATOM 725 HB3 AIB A 48 23.257 12.333 20.378 1.00 0.00
> H
> ATOM 726 HB4 AIB A 48 23.978 13.693 23.752 1.00 0.00
> H
> ATOM 727 HB5 AIB A 48 22.403 13.247 24.451 1.00 0.00
> H
> ATOM 728 HB6 AIB A 48 23.583 11.981 24.034 1.00 0.00
> H
>
>
> If anyone knows how to help me, that would be great! Thank you so much.
>
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Received on Tue Sep 10 2024 - 18:30:02 PDT
