Dear Eduardo,
Sorry to interfere in your discussion, but did you take into account that
by including 40 hydronium ion the pH of your system will be unrealistic,
unless the system volume will range between 1E+19 to 1E+24 cubic angstrom?
Greeting,
Hector.
> Dear Bill Ross,
>
> I'll follow your suggestions. Thank you for your help.
>
> Sincerely,
>
> Eduardo.
>
>
>
>
>
> ________________________________
> De: Bill Ross <ross.cgl.ucsf.edu>
> Enviado: quarta-feira, 6 de janeiro de 2021 23:59
> Para: amber.ambermd.org <amber.ambermd.org>
> Assunto: Re: [AMBER] How does the xleap/teap recognize the H3O+
> (hydronium) ions?
>
> One way to quickly sidestep the issue is to edit the residue name in
> your pdb, since the truncated one is still unique.
>
> If so, make sure everything aligns, and when in doubt, try something and
> it will become more obvious either way.
>
> On 1/6/21 6:56 PM, Bill Ross wrote:
>> Those are atom names, the residues are in a different list. If Amber has
>> taught anyone anything about life, I hope "When in doubt, try it" is on
>> the list. If ambpdb works, that means the residue name is intact in
>> prmtop and there's no need to check.
>>
>> Maybe the 4-char-ness of the resname is the main issue.
>>
>> All the atoms are in .rst, it's just an issue of mapping to names.
>>
>>
>> On 1/6/21 6:37 PM, Eduardo R. Almeida wrote:
>>> In my prmtop, the H3O+ ion is indicated by the letter "O":
>>>
>>> ...
>>> Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+
>>> Na+ Na+
>>> Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ K+ K+ K+
>>> K+ MG
>>> MG MG Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl-
>>> Cl- Cl-
>>> Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl-
>>> Cl- Cl-
>>> Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- Cl- O O O O O O O O
>>> O O
>>> O O O O O O O O O O O O O O O O O O
>>> O O
>>> O O O O O O O O O O O H1 H2 O H1 H2 O H1
>>> H2 O
>>> H1 H2 O H1 H2 O H1 H2 O H1 H2 O H1 H2 O H1 H2 O
>>> H1 H2
>>> ...
>>>
>>> This is strange. Anyway, should I use the ambpdb for generating the pdb
>>> file? In this case, the command would be:
>>>
>>> ambpdb -p file.prmtop <file.rst> new.pdb
>>>
>>> Since I need the last frame of my trajectory, the file.rst would
>>> contain this last structure of my trajectory?
>>>
>>>
>>> -------------------------------------------------------------------------------
>>> Eduardo R. Almeida
>>> Estudante de Doutorado em Qu?mica
>>> N?cleo de Estudos em Qu?mica Computacional (NEQC)
>>> Universidade Federal de Juiz de Fora (UFJF)
>>> Juiz de Fora - MG - Brasil
>>>
>>>
>>>
>>>
>>> ________________________________
>>> De: Bill Ross <ross.cgl.ucsf.edu>
>>> Enviado: quarta-feira, 6 de janeiro de 2021 23:24
>>> Para: amber.ambermd.org <amber.ambermd.org>
>>> Assunto: Re: [AMBER] How does the xleap/teap recognize the H3O+
>>> (hydronium) ions?
>>>
>>> I forgot leap added the ions. :-)
>>>
>>> What resname is in your prmtop? If it's H3O+, I'd try generating the
>>> pdb
>>> with ambpdb.
>>>
>>> I suspect '+' may not be valid in a residue name by the PDB standard
>>> and/or some coding convention.
>>>
>>> Bill
>>>
>>> On 1/6/21 6:18 PM, Eduardo R. Almeida wrote:
>>>> 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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--------------------------------------
Dr. Hector A. Baldoni
Profesor Titular (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
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Received on Wed Jan 06 2021 - 19:30:03 PST
