Hello,
I ended up solving this! The problem was with the names of the atoms in
the pdb file (instead of naming CB1 it was just CB). Now tleap is working.
But thank you for offering some help🙂
Best,
Rosa
Am 11/09/2024 um 3:12 schrieb 王世玉:
> 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.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> </cb></aib></hb1></aib></cb1></aib></cb1></aib></aib></hb1></aib></cb></aib></hb1></aib></cb1></aib></aib></amber.ambermd.org>
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Received on Wed Sep 11 2024 - 07:30:02 PDT
