Regarding my pdb file generated by using cpptraj, the H3O+ was indicated as:
...
ATOM 40091 O 3O+ 1131 53.333 68.934 230.485 1.00 0.00 O
TER
ATOM 40092 O 3O+ 1132 1.010 63.086 148.343 1.00 0.00 O
TER
ATOM 40093 O 3O+ 1133 28.450 29.000 15.985 1.00 0.00 O
TER
ATOM 40094 O 3O+ 1134 33.720 19.364 259.483 1.00 0.00 O
TER
ATOM 40095 O 3O+ 1135 43.554 59.022 110.119 1.00 0.00 O
TER
ATOM 40096 O 3O+ 1136 58.459 44.400 302.693 1.00 0.00 O
TER
ATOM 40097 O 3O+ 1137 54.367 60.589 149.876 1.00 0.00 O
TER
ATOM 40098 O 3O+ 1138 21.787 59.751 146.889 1.00 0.00 O
TER
ATOM 40099 O 3O+ 1139 50.446 54.713 265.513 1.00 0.00 O
TER
ATOM 40100 O 3O+ 1140 0.091 66.957 261.158 1.00 0.00 O
...
________________________________
De: Eduardo R. Almeida <eduardoe.r.a.hotmail.com>
Enviado: quarta-feira, 6 de janeiro de 2021 22:28
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions?
Dear Bill Ross,
Thank you for your help.
I tried to use the command that you suggested:
*************************************************************************************
>> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second,
>> frcmod14SB = loadamberparams frcmod.ff14SB
>> gaff = loadamberparams gaff2.dat
>> # ----- leaprc for loading the ff14SB force field
>> # ----- leaprc for loading the general Amber Force field.
>> # leaprc for loading the Lipid17 v1.1 force field
>> lipid17 = loadamberparams lipid17.dat
>> loadAmberParams frcmod.ions1lm_126_tip3p
>> loadAmberParams frcmod.ions234lm_126_tip3p
> loadamberparams frcmod.ionsjc_tip3p
>> loadAmberParams frcmod.ionsjc_tip3p
>> loadAmberParams frcmod.tip3p
>> # load atom type hybridizations
>> # Load atom type hybridizations
Loading: ACE
Loading: Ag
Loading: AG
Loading: AL
Loading: ALA
Loading: AR
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: BA
Loading: Be
Loading: BR
Loading: CA
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CD
Loading: Ce
Loading: CE
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHCL3BOX
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHL
Loading: CHYP
Loading: CILE
Loading: Cl-
Loading: CL
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CO
Loading: CPHE
Loading: CPRO
Loading: Cr
Loading: CR
Loading: CS
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CU
Loading: CU1
Loading: CVAL
Loading: CYM
Loading: CYS
Loading: CYX
Loading: DC4
Loading: DHA
Loading: Dy
Loading: Er
Loading: EU
Loading: EU3
Loading: F
Loading: FB3
Loading: FB3BOX
Loading: FB4
Loading: FB4BOX
Loading: FE
Loading: FE2
Loading: GD3
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: H3O+
Loading: HE+
Loading: Hf
Loading: HG
Loading: HID
...
**********************************
Do you think that this error is related to the fact that the residue name of the hydronium ion should have 4 digits (H3O+), but in the pdb file, the rule is to use only 3 letters (3O+)?
Sincerely,
Eduardo.
-
________________________________
De: Bill Ross <ross.cgl.ucsf.edu>
Enviado: quarta-feira, 6 de janeiro de 2021 22:08
Para: amber.ambermd.org <amber.ambermd.org>
Assunto: Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions?
'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.
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
--
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Received on Wed Jan 06 2021 - 18:00:02 PST
