Saranya,
the problems arise because leap always converts the first and the last
residue in a protein chain into terminal ones and then uses the
structure and parameters before saving. And then, your additional bond
does not fit into this scheme any more.
The solution is to prevent leap from automatically changing the
'terminal' residues into their terminal instances.
This has been asked and answered here in the past already.
A simple way, at least in my opinion, which also is applicable in your
case (small peptide), would be to use the leap command
loadpdbusingseq (cf Amber manual 14.6.28):
Here, you specify the amino acid sequence explicitely for your pdb file
to load; if you do not use the terminal residue names like NALA or CGLY,
tleap keeps the mid-term residues also at the termini, and your bond
command should work fine.
Best regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 17.02.2022 um 11:19 schrieb saranya.cbmm.lodz.pl:
> Hi,
>
> I am performing the MD simulation for cyclic 22-residue peptide using
> ABMER 20. Initially the structure was minimized for 100ns by using
> Gromacs-2021. The conformer structure of the cyclic peptide contains a
> bond between N and C terminus. While I’m using the conformer structure
> to generate the parameter files for the amber simulation by using xleap
> interface the bond was missing because the amber automatically added the
> hydrogen at the N and C terminals. So I'm using the command "bond
> prot.1.N prot.22.C" to manually draw the bond between the terminals, but
> when I try to save the settings, I get the following error.
>
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
>
> Error: Could not find bond parameter for: N3 - C
> Building angle parameters.
>
> Error: Could not find angle parameter: CX - N3 - C
>
> Error: Could not find angle parameter: H - N3 - C
>
> Error: Could not find angle parameter: N3 - C - CX
>
> Error: Could not find angle parameter: N3 - C - O2
> Building proper torsion parameters.
>
> Error: ** No torsion terms for CX-N3-C-CX
>
> Error: ** No torsion terms for CX-N3-C-O2
>
> Error: ** No torsion terms for H-N3-C-CX
>
> Error: ** No torsion terms for H-N3-C-O2
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for CX-O2-C-N3
> atoms are: CA O C N
> total 65 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
> Warning: Parameter file was not saved.
>
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Received on Thu Feb 17 2022 - 03:30:02 PST
