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 - 03:30:02 PDT
