If you e.g.
$ grep -i load leap.log | sort -u
in the directory where you neutralized, one of the loads will be for
whatever file your residue called "30+" was defined in.
Bill
On 1/6/21 3:15 PM, Eduardo R. Almeida wrote:
> 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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--
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Received on Wed Jan 06 2021 - 17:30:02 PST
