Loading PDB file:
./3HVH.pdb
(starting new molecule for chain
)
total atoms in file:
3439
(using default radius 1.500000 for
MG)
Solute vdw bounding box: 40.691 43.566
56.381
Total bounding box for atom centers: 56.691 59.566
72.381
Solvent unit box: 18.774 18.774
18.774
(using default radius 1.500000 for
MG)
Total vdw box size: 59.898 62.546 75.322
angstroms.
Volume: 282183.092
A^3
Mass > 135575.846 amu, Density > 0.798
g/cc
(type - hence mass - of one or more atoms could not be
found)
Added 6163 residues.
There is also this in the output
On Thu, 27 Sep 2018 at 15:08, Keiran Corbett <keirancorbett.gmail.com>
wrote:
> Thank you for the reply.
>
> It is a pdb file I have prepped in MOE
> I use tip3p for my sourced file.
>
> Building topology.
> Building atom parameters.
> For atom: .R<MG 259>.A<MG 1> Could not find vdW (or other) parameters for
> type: Mg2+
>
> I get this error in tleap and this is what I typed
> (It is a slightly older version of AMBER but that can't be changed at this
> point)
> source leaprc.gaff
> source leaprc.ff14SB
> source leaprc.tip3p
> gaff=loadamberparams gaff.dat
> LIG=loadmol2 3HVHL.mol2
> loadamberparams 3HVHL.frcmod
> saveoff LIG 3HVHL.lib
> loadoff 3HVHL.lib
> complex=loadpdb 3HVH.pdb
> solvatebox complex TIP3PBOX 8.0
> loadamberparams frcmod.ionsjc_tip3p
> addIons2 complex Na+ 0
> addIons2 complex Cl- 0
> saveamberparm complex 3HVH.prmtop 3HVH.crd
> quit
>
>
> On Thu, 27 Sep 2018 at 13:53, David Case <david.case.rutgers.edu> wrote:
>
>> On Thu, Sep 27, 2018, Keiran Corbett wrote:
>>
>> > I have counter ions i.e. Mg2+ in the binding site of my protein-ligand
>> > strucuture determined by X-ray crystallography.
>> > I wondered what people thought was the best way to deal with this as
>> AMBER
>> > doesn't recognise these kind of counter ions.
>>
>> Amber should recognize these MG ions, assuming that you have sourced a
>> leaprc.water.xxxx file in your tleap input. If you are seeing problems,
>> we
>> would need to know details: esp. is this a "standard" pdb file from the
>> PDB
>> website? Or might it be a file with non-standard atom or residue names?
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Sep 27 2018 - 08:00:02 PDT
