Hello,
Thanks for your reply. When I upload the protonated pdb file (using loadpdb in tleap)
I get following error (truncated):
Joining GLU - BLA
Created a new atom named: CHA within residue: .R<BLA 297>
Created a new atom named: NA within residue: .R<BLA 297>
Created a new atom named: C1A within residue: .R<BLA 297>
Created a new atom named: C2A within residue: .R<BLA 297>
Created a new atom named: C3A within residue: .R<BLA 297>
Created a new atom named: C4A within residue: .R<BLA 297>
Created a new atom named: CMA within residue: .R<BLA 297>
Created a new atom named: CAA within residue: .R<BLA 297>
Created a new atom named: CBA within residue: .R<BLA 297>
Created a new atom named: CGA within residue: .R<BLA 297>
Created a new atom named: O1A within residue: .R<BLA 297>
…
….
….
Added missing heavy atom: .R<BLA 297>.A<C1 1>
Added missing heavy atom: .R<BLA 297>.A<C29 2>
Added missing heavy atom: .R<BLA 297>.A<C2 39>
Added missing heavy atom: .R<BLA 297>.A<N4 3>
Added missing heavy atom: .R<BLA 297>.A<C28 23>
Added missing heavy atom: .R<BLA 297>.A<N1 40>
Added missing heavy atom: .R<BLA 297>.A<C3 43>
Added missing heavy atom: .R<BLA 297>.A<C26 4>
Added missing heavy atom: .R<BLA 297>.A<C27 22>
Added missing heavy atom: .R<BLA 297>.A<C31 24>
Added missing heavy atom: .R<BLA 297>.A<C5 41>
Added missing heavy atom: .R<BLA 297>.A<C4 42>
Added missing heavy atom: .R<BLA 297>.A<C7 44>
Added missing heavy atom: .R<BLA 297>.A<C25 5>
Added missing heavy atom: .R<BLA 297>.A<C30 33>
Added missing heavy atom: .R<BLA 297>.A<C32 25>
> desc complex.2.SG
ATOM
Normal Perturbed
Name: SG SG
Type: SH SH
Charge: -0.3119 0.000
Polarization: 0.0000 0.000
Element: S (not affected by pert)
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: 4.573000, 30.145000, 27.611000
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<CYS 2>.A<CB 5> by a single bond.
Bonded to .R<CYS 2>.A<HG 9> by a single bond.
> desc complex.297.C24
ATOM
Name: C24
Type: c2
Charge: -0.4046
Polarization: 0.0000
Element: C
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: 16.907726, 12.776802, 40.597918
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<BLA 297>.A<C23 11> by a single bond.
Bonded to .R<BLA 297>.A<H15 13> by a single bond.
>
> # bond these two entities:
>
> bond complex.2.SG complex.297.C24
> saveamberparm complex complex.prmtop complex.inpcrd
Checking Unit.
WARNING: There is a bond of 24.949144 angstroms between:
------- .R<CYS 2>.A<SG 8> and .R<BLA 297>.A<C24 12>
WARNING: The unperturbed charge of the unit: -3.000004 is not zero.
FATAL: Atom .R<BLA 297>.A<CHA 76> does not have a type.
FATAL: Atom .R<BLA 297>.A<NA 77> does not have a type.
FATAL: Atom .R<BLA 297>.A<C1A 78> does not have a type.
FATAL: Atom .R<BLA 297>.A<C2A 79> does not have a type.
FATAL: Atom .R<BLA 297>.A<C3A 80> does not have a type.
FATAL: Atom .R<BLA 297>.A<C4A 81> does not have a type.
FATAL: Atom .R<BLA 297>.A<CMA 82> does not have a type.
FATAL: Atom .R<BLA 297>.A<CAA 83> does not have a type.
FATAL: Atom .R<BLA 297>.A<CBA 84> does not have a type.
FATAL: Atom .R<BLA 297>.A<CGA 85> does not have a type.
FATAL: Atom .R<BLA 297>.A<O1A 86> does not have a type.
FATAL: Atom .R<BLA 297>.A<O2A 87> does not have a type.
FATAL: Atom .R<BLA 297>.A<CHB 88> does not have a type.
FATAL: Atom .R<BLA 297>.A<NB 89> does not have a type.
FATAL: Atom .R<BLA 297>.A<C1B 90> does not have a type.
FATAL: Atom .R<BLA 297>.A<C2B 91> does not have a type.
FATAL: Atom .R<BLA 297>.A<C3B 92> does not have a type.
FATAL: Atom .R<BLA 297>.A<C4B 93> does not have a type.
FATAL: Atom .R<BLA 297>.A<CMB 94> does not have a type.
FATAL: Atom .R<BLA 297>.A<OB 95> does not have a type.
FATAL: Atom .R<BLA 297>.A<CAB 96> does not have a type.
FATAL: Atom .R<BLA 297>.A<CBB 97> does not have a type.
FATAL: Atom .R<BLA 297>.A<NC 98> does not have a type.
FATAL: Atom .R<BLA 297>.A<C1C 99> does not have a type.
FATAL: Atom .R<BLA 297>.A<C2C 100> does not have a type.
FATAL: Atom .R<BLA 297>.A<C3C 101> does not have a type.
FATAL: Atom .R<BLA 297>.A<C4C 102> does not have a type.
FATAL: Atom .R<BLA 297>.A<CMC 103> does not have a type.
FATAL: Atom .R<BLA 297>.A<OC 104> does not have a type.
FATAL: Atom .R<BLA 297>.A<CAC 105> does not have a type.
FATAL: Atom .R<BLA 297>.A<CBC 106> does not have a type.
FATAL: Atom .R<BLA 297>.A<CHD 107> does not have a type.
FATAL: Atom .R<BLA 297>.A<ND 108> does not have a type.
FATAL: Atom .R<BLA 297>.A<C1D 109> does not have a type.
FATAL: Atom .R<BLA 297>.A<C2D 110> does not have a type.
FATAL: Atom .R<BLA 297>.A<C3D 111> does not have a type.
FATAL: Atom .R<BLA 297>.A<C4D 112> does not have a type.
FATAL: Atom .R<BLA 297>.A<CMD 113> does not have a type.
FATAL: Atom .R<BLA 297>.A<CAD 114> does not have a type.
FATAL: Atom .R<BLA 297>.A<CBD 115> does not have a type.
FATAL: Atom .R<BLA 297>.A<CGD 116> does not have a type.
FATAL: Atom .R<BLA 297>.A<O1D 117> does not have a type.
FATAL: Atom .R<BLA 297>.A<O2D 118> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMD3 119> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMD2 120> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMD1 121> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMC3 122> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMC2 123> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMC1 124> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMB3 125> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMB2 126> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMB1 127> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMA3 128> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMA2 129> does not have a type.
FATAL: Atom .R<BLA 297>.A<HMA1 130> does not have a type.
FATAL: Atom .R<BLA 297>.A<HBD2 131> does not have a type.
FATAL: Atom .R<BLA 297>.A<HBD1 132> does not have a type.
FATAL: Atom .R<BLA 297>.A<HBC1 133> does not have a type.
FATAL: Atom .R<BLA 297>.A<HBB2 134> does not have a type.
FATAL: Atom .R<BLA 297>.A<HBB1 135> does not have a type.
FATAL: Atom .R<BLA 297>.A<HBA2 136> does not have a type.
FATAL: Atom .R<BLA 297>.A<HBA1 137> does not have a type.
FATAL: Atom .R<BLA 297>.A<HAD2 138> does not have a type.
FATAL: Atom .R<BLA 297>.A<HAD1 139> does not have a type.
FATAL: Atom .R<BLA 297>.A<HAA2 140> does not have a type.
FATAL: Atom .R<BLA 297>.A<HAA1 141> does not have a type.
FATAL: Atom .R<BLA 297>.A<HHD 142> does not have a type.
FATAL: Atom .R<BLA 297>.A<HHB 143> does not have a type.
FATAL: Atom .R<BLA 297>.A<HHA 144> does not have a type.
FATAL: Atom .R<BLA 297>.A<HC 145> does not have a type.
FATAL: Atom .R<BLA 297>.A<HB 146> does not have a type.
FATAL: Atom .R<BLA 297>.A<HAC 147> does not have a type.
FATAL: Atom .R<BLA 297>.A<HAB 148> does not have a type.
FATAL: Atom .R<BLA 297>.A<HA 149> does not have a type.
FATAL: Atom .R<BLA 297>.A<H 150> does not have a type.
Failed to generate parameters
Parameter file was not saved.
>
>
> desc complex.2.SG
ATOM
Normal Perturbed
Name: SG SG
Type: SH SH
Charge: -0.3119 0.000
Polarization: 0.0000 0.000
Element: S (not affected by pert)
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: 4.573000, 30.145000, 27.611000
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<CYS 2>.A<CB 5> by a single bond.
Bonded to .R<CYS 2>.A<HG 9> by a single bond.
Bonded to .R<BLA 297>.A<C24 12> by a single bond.
>
> desc complex.297.C24
ATOM
Name: C24
Type: c2
Charge: -0.4046
Polarization: 0.0000
Element: C
Atom flags: (decimal 131072 hex 0x20000)
posfxd n posblt n posdrwn n selected n
pert n notdisp n touched n posknwn Y
internal n needsmin n needsbuild n
Atom position: 16.907726, 12.776802, 40.597918
Atom velocity: 0.000000, 0.000000, 0.000000
Bonded to .R<BLA 297>.A<C23 11> by a single bond.
Bonded to .R<BLA 297>.A<H15 13> by a single bond.
Bonded to .R<CYS 2>.A<SG 8> by a single bond.
The cys (with which the ligand (BLA) is supposed to be bonded) has added Hydrogens by leap. In an another attempt, I tried changing the atom names with respect to the PDB thats generated during the prepgen step,
that didn’t work too. I would like to know the clean way to change the atom-types of my ligand in the complex without compromising the bonds and charges.
It also says, the unperturbed charge on the residue is -3 and not sure how to maintain the charge of my ligand.
Thank you,
Sincerely,
Sivasudhan R
> On 13 Feb 2018, at 14:47, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> What are the exact error/warning messages your are getting from leap?
>
> -Dan
>
> On Tue, Feb 13, 2018 at 2:22 AM, Sivasudhan R <sivasudhan.rath.gmail.com> wrote:
>> Dear Amber users,
>> I am a novice user with Antechamber. I have a system in which the ligand (76 atoms, with netcharge -1) is covalently connected to the protein (CYS:SG).
>> I am interested in generating a parameter file for protein+ligand (complex) . I could generate .prmtop and .inpcrd files for the ligand separately. The problem occurs when I try for the complex!
>>
>> Used pd4amber —reduce , [removed ligand coord] and added a hydrogen (for protonation) and a capping hydrogen (H33) > ligand-capped.pdb : Netcharge -1 /singlet
>>
>> During the parametrization of the ligand (a non-standard residue) :
>> antechamber -i lig.log -fi gout -fo ac -o lig.ac -c resp -nc -1 -rn LIG -at gaff
>>
>> I have prepgen file
>> [to remove capping H and to tell that it will be connected to CYS of the protein]
>> Lig.mc
>> HEAD_GROUP C24
>> OMIT_NAME H33
>> PRE_HEAD_TYPE SG
>> CHARGE -1.0
>>
>> prepgen -i lig.ac -m Lig.mc -o lig.prepin -f int (I get NEWPDB.PDB , using this as a reference PDB for ligand)
>>
>> parmchk -i lig.prepin -f prepi -o lig.frcmod
>>
>> In leap:
>> source leaprc.gaff
>> source leaper.protein.ff14SB
>> Loadamberprep lig.prepin
>> Loadamberparams lig.frcmod
>> x = loadpdb complex.pdb
>> desc x.297.C24. (of ligand)
>> desc x.2.SG. (of protein: (tleap adds additional H, filling the valence of CYS 2:SG))
>> bond x.297.C24 x.2.SG
>> saveoff x complex.lib
>> Loadoff complex.lib
>> saveamberparm x complex.prmtop complex.inpcrd
>>
>> I get an error saying atomtypes are missing. I also manually edited the PDB (the ligand part) with no success . I am not sure, if my procedure was correct.
>>
>> Also, I would like to know the protocol for changing the atom type of subset of atoms (ligand) in a complex.pdb Is the bonding step required (I do it because, in the prepgen, after omitting the H33, it said use bond command to bond) given that I load a complex.pdb (where the protein and ligand are bonded)
>>
>> Kindly help.
>>
>> Thank you,
>>
>>
>> Sincerely,
>>
>> Sivasudhan R
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Feb 13 2018 - 07:00:04 PST
