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
>>> --
>>> Phobrain.com
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> Phobrain.com
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> --
> Phobrain.com
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Phobrain.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 06 2021 - 19:00:02 PST
