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.
_________________________________________________________________
Find love online with MSN Personals.
http://match.msn.com.my/match/mt.cfm?pg=channel
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 01 2005 - 05:53:01 PST
