Dear Amber Users,
I am struggling with processing the results from the MD simulation for the system with three non-standard residues. The system is quite big - 1255 amino acids in total. To be more specific, it's the acyl-enzyme complex, in which we have two big macromolecules - a receptor in which one of the loops is cleaved and the protease which is responsible for this cleavage.
Since it is the intermediate state of the reaction, the peptide bond in the receptor part is already cleaved but one amino acid from the cleavage site of the receptor is connected with the protease via the ester bond.
My problem is that when I process the trajectory file with cpptraj and when I open the .nc file in vmd, I can't see the three non-standard residues in the sequence and I observe the gaps in the structure. Also, when I performed the rmsf analysis of the trajectory, in the output file there is no rmsf value for these three residues. However, when I extracted the example frame from the created .nc file, non-standard residues are present in the .pdb file. Right now I am also wondering if those residues are even taken into consideration during the MD simulation (although when I created input .prmtop and .inpcrd files including the parameters for non-standard residues I didn't get any errors in tleap and also the simulation ended without any errors).
I noticed in the output file from the cpptraj the following warnings:
Warning: 1 molecules have non-contiguous segments of atoms.
1 2 segments: 1-6865 (6865) 12658-19658 (7001)
Warning: The 'fixatomorder' command can be used to reorder the topology and any
Warning: associated coordinates.
Atom number 6865 is the last atom of one of the non-standard residues from the proteolytic cleavage site (this amino acid was connected with the protease using the bond command during the preparation of input files in tleap); in the original .pdb file which I used for the preparation of the .prmtop and .inpcrd files there is a TER after this atom.
Atoms 12658-19658 include the whole range of amino acids from protease. In the original .pdb file, before and after protease there were TERs.
Do you have any idea what can be the problem or what should I try in order to process the trajectory in the correct way and be able to see the non-standard residues and also proceed with rmsf analysis for them? Should I use this fixatomorder command? If so, can you give me suggestions how to properly use that? I saw that there is an option "pdborder" but it's described as experimental.
Below you can find the input for the cpptraj I am using:
parm *.prmtop
reference*.inpcrd
trajin prod1.nc
trajin prod2.nc
trajin prod3.nc
trajin prod4.nc
trajin prod5.nc
trajin prod6.nc
trajin prod7.nc
trajin prod8.nc
trajin prod9.nc
trajin prod10.nc
#autoimage
center :1-1255 mass origin
image origin center familiar
strip :WAT,Cl-,Na+ outprefix nowat
rms ToRef :
1-1255.CA,C,N reference out rmsd_100ns_x1.arg mass
#rms ToRef :
1-1255.CA reference out rmsd_CA.arg mass
atomicfluct out rmsf_CA_100ns_x1.arg :
1-1255.CA byres
atomicfluct out rmsf_100ns_x1.arg :
1-1255.CA,C,N byres
trajout *_nowat.nc NetCDF
go
Attached, please find the .out file from cpptraj.
Thank you in advance for your help.
Best
Maria Bzówka
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Received on Sat Aug 12 2023 - 02:00:02 PDT
