Dear Bill Ross,
Actually, my original pdb file does not contain this ion. When I firstly loaded the pdb file in xleap, the charge of my system was -40.0. Thus, I neutralized this system with H3O+ ions:
addions2 mem H3O+ 0
Then I saved this pdb file in xleap:
***********************************
...
TER
ATOM 40091 O H3O 1131 20.894 54.792 127.101 1.00 0.00
TER
ATOM 40092 O H3O 1132 62.894 37.792 205.101 1.00 0.00
TER
ATOM 40093 O H3O 1133 24.894 15.792 83.101 1.00 0.00
TER
ATOM 40094 O H3O 1134 11.894 51.792 205.101 1.00 0.00
TER
ATOM 40095 O H3O 1135 63.894 53.792 83.101 1.00 0.00
TER
ATOM 40096 O H3O 1136 20.894 52.792 250.101 1.00 0.00
TER
ATOM 40097 O H3O 1137 58.894 55.792 204.101 1.00 0.00
TER
ATOM 40098 O H3O 1138 24.894 14.792 206.101 1.00 0.00
TER
ATOM 40099 O H3O 1139 54.894 51.792 129.101 1.00 0.00
TER
ATOM 40100 O H3O 1140 66.894 52.792 207.101 1.00 0.00
TER
ATOM 40101 O H3O 1141 11.894 52.792 82.101 1.00 0.00
TER
ATOM 40102 O H3O 1142 62.894 38.792 81.101 1.00 0.00
TER
ATOM 40103 O H3O 1143 34.894 36.792 131.101 1.00 0.00
TER
...
*****************************************
I tried to use this name "H3O", but I got the same error in xleap.
It seems the xleap included the ions when I asked to neutralized the system, but it did not accept the pdb file (actually the H3O+ ions) when I tried to submit the same file for a new simulation.
________________________________
De: Bill Ross <ross.cgl.ucsf.edu>
Enviado: quarta-feira, 6 de janeiro de 2021 23:03
Para: amber.ambermd.org <amber.ambermd.org>
Assunto: Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions?
Looks like the residue name was truncated at some point. Was it the same in your original pdb?
> Loading: H3O+
On 1/6/21 5:33 PM, Eduardo R. Almeida wrote:
> 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 - 18:30:02 PST
