Dear Amber users,
Recently, by using the xleap, I neutralized a system with H3O+ ions and then, I conducted a molecular dynamics simulation of this system (310.0 K, 1.0 bar for 400 ns). Since I need to use this system (lipid bilayer) in a new simulation (inclusion of a drug molecule), I generated a pdb file from the last frame of this simulation. However, when I tried to prepare this new system (lipid bilayer + drug) by loading the pdb file of the membrane, I got some warnings and errors in xleap:
*****************************************************************************
...
Matching PDB residue names to LEaP variables.
Warning: Unknown residue: 3O+ number: 1130 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: 3O+ number: 1131 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: 3O+ number: 1132 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: 3O+ number: 1133 type: Terminal/last
..relaxing end constraints to try for a dbase match
...
Warning: -no luck
Creating new UNIT for residue: 3O+ sequence: 1131
Created a new atom named: O within residue: .R<3O+ 1131>
Creating new UNIT for residue: 3O+ sequence: 1132
Created a new atom named: O within residue: .R<3O+ 1132>
Creating new UNIT for residue: 3O+ sequence: 1133
Created a new atom named: O within residue: .R<3O+ 1133>
Creating new UNIT for residue: 3O+ sequence: 1134
Created a new atom named: O within residue: .R<3O+ 1134>
Creating new UNIT for residue: 3O+ sequence: 1135
Created a new atom named: O within residue: .R<3O+ 1135>
Creating new UNIT for residue: 3O+ sequence: 1136
Created a new atom named: O within residue: .R<3O+ 1136>
Creating new UNIT for residue: 3O+ sequence: 1137
Created a new atom named: O within residue: .R<3O+ 1137>
...
*******************************************************************************
It seems the xleap does not recognize the name of this H3O+ ion located in this pdb file. It is worth to mention that I generated this pdb file by using the cpptraj.
Could anyone help me with this problem?
Sincerely,
Eduardo.
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Received on Wed Jan 06 2021 - 15:30:02 PST
