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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Received on Wed Jan 06 2021 - 18:30:03 PST
