AMBER Archive (2005)

Subject: Re: AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!!

From: Jiri Matousek (matousek_at_chemi.muni.cz)
Date: Fri Apr 01 2005 - 01:37:39 CST

Hi Chaiann,
You have loaded parametres for solute, but parameters for chloroform
CHCL3BOX are in frcmod.chcl3 file, these have to be loaded too:

loadamberparams frcmod.chcl3

I hope this helps.
Jiri Matousek

chaiann ng wrote:

> Dear Amber User
>
> I am trying to solvate my molecule in a box of chcl3, xleap can read
> in solvateoct mymolecule CHCL3BOX 10, but this message appear
>
>> solvateoct VVA CHCL3BOX 10
>
> Scaling up box by a factor of 1.266491 to meet diagonal cut criterion
> Solute vdw bounding box: 11.319 16.451 10.635
> Total bounding box for atom centers: 41.781 41.781 41.781
> (box expansion for 'iso' is 32.4%)
> Solvent unit box: 56.496 56.496 56.496
> (using default radius 1.500000 for CL1)
> (using default radius 1.500000 for CL2)
> (using default radius 1.500000 for CL3)
> (using default radius 1.500000 for CL1)
> (using default radius 1.500000 for CL2)
> (using default radius 1.500000 for CL3)
> repeating for quite long.
>
> Volume: 39149.547 A^3 (oct)
> Mass > 3220.316 amu, Density > 0.137 g/cc
> (type - hence mass - of one or more atoms could not be found)
> Added 207 residues.
>
> ----------
> when I go edit my molecule, the chcl3 molecule is green colour, so I
> select one of them, edit it, under element type C1 and H1 is ? ? ,
> instead of C and H.
>
>
> If I go ahead and save the parameter file, this is what happen
>
>> saveamberparm VVA vm1.prmtop vm1.inpcrd
>
> Checking Unit.
> Building topology.
> Building atom parameters.
> For atom: .R<CL3 2>.A<CL1 3> Could not find type: CL
> For atom: .R<CL3 2>.A<CL2 4> Could not find type: CL
> For atom: .R<CL3 2>.A<CL3 5> Could not find type: CL
> For atom: .R<CL3 3>.A<CL1 3> Could not find type: CL
> For atom: .R<CL3 3>.A<CL2 4> Could not find type: CL
> For atom: .R<CL3 3>.A<CL3 5> Could not find type: CL
> For atom: .R<CL3 4>.A<CL1 3> Could not find type: CL
> For atom: .R<CL3 4>.A<CL2 4> Could not find type: CL
> For atom: .R<CL3 4>.A<CL3 5> Could not find type: CL
> For atom: .R<CL3 5>.A<CL1 3> Could not find type: CL
> For atom: .R<CL3 5>.A<CL2 4> Could not find type: CL
> For atom: .R<CL3 5>.A<CL3 5> Could not find type: CL
> For atom: .R<CL3 6>.A<CL1 3> Could not find type: CL
> For atom: .R<CL3 6>.A<CL2 4> Could not find type: CL
> For atom: .R<CL3 6>.A<CL3 5> Could not find type: CL
> Repeating for quite long
> Parameter file was not saved.
>
> So, I could not save prmtop and inpcrd file.
>
> Is anyone come across the same problem?
> I am using Amber 8 on linux. I load in leaprc.gaff and leaprc.ff03
> (same thing happen if i use leaprc.ff99)
>
> Please give me some advice.
>
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