'3O+' not '30+', sorry.
On 1/6/21 5:06 PM, Bill Ross wrote:
> 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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Received on Wed Jan 06 2021 - 17:30:03 PST
