Hi Dan,
I used tleap to generate the top files. The following is the script. I
think the DX, DY, DZ atoms are complexed with the Mg ions (like the EPW in
water molecules?), but I have no idea what they are and why the mass is 3...
source leaprc.ff12SB
source leaprc.gaff
addAtomTypes {
{ "MM" "Mg" "sp3" }
{ "DX" "Mg" "sp3" }
{ "DY" "Mg" "sp3" }
{ "DZ" "Mg" "sp3" }
}
loadamberparams frcmod.dummymg
loadoff md6.off
MG = MD6
loadamberparams frcmod_s2p
loadoff S2P.off
loadamberparams frcmod_t2p
loadoff T2P.off
loadamberparams ADP.frcmod
loadoff ADP.lib
loadoff ions08.lib
com=loadpdb 3TNP-with2ADP2MG.pdb
loadAmberParams frcmod.tip4pew
solvatebox com TIP4PEWBOX 12
loadamberparams frcmod.ionsjc_tip4pew
addionsrand com K+ 0
addionsrand com K+ 131
addionsrand com Cl- 131
saveamberparm com 3TNP-with2ADP2MG.prmtop 3TNP-with2ADP2MG.inpcrd
quit
Here's one of the Mg ion complex in the pdb file generated by the topology
files.
ATOM 19744 MD MD6 1218 48.004 54.386 47.064 1.00
0.00 M
ATOM 19745 DX1 MD6 1218 48.878 54.386 47.064 1.00
0.00 D
ATOM 19746 DY1 MD6 1218 48.005 54.441 46.151 1.00
0.00 D
ATOM 19747 DY2 MD6 1218 48.005 54.441 47.976 1.00
0.00 D
ATOM 19748 DX2 MD6 1218 47.131 54.410 47.064 1.00
0.00 D
ATOM 19749 DZ1 MD6 1218 47.991 53.448 47.064 1.00
0.00 D
ATOM 19750 DZ2 MD6 1218 48.017 55.350 47.064 1.00
0.00 D
Thanks,
Richard
On Mon, Aug 5, 2013 at 4:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Aug 5, 2013 at 1:41 PM, Hailin Huang
> <hailin.huang.my.liu.edu<javascript:;>>
> wrote:
> > Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> > Warning: Could not determine atomic number from name [DX1 ]
>
> Are you sure you are supposed to have atoms in your system with masses of
> 3.0? Unless they're some isotope like tritium this (as well as the atom
> names themselves) seems strange. How did you create this topology?
>
> -Dan
>
> > Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> > Warning: Could not determine atomic number from name [DY1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> > Warning: Could not determine atomic number from name [DY2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> > Warning: Could not determine atomic number from name [DX2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> > Warning: Could not determine atomic number from name [DZ1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> > Warning: Could not determine atomic number from name [DZ2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> > Warning: Could not determine atomic number from name [DX1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> > Warning: Could not determine atomic number from name [DY1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> > Warning: Could not determine atomic number from name [DY2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> > Warning: Could not determine atomic number from name [DX2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> > Warning: Could not determine atomic number from name [DZ1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> > Warning: Could not determine atomic number from name [DZ2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> > Warning: Could not determine atomic number from name [DX1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> > Warning: Could not determine atomic number from name [DY1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> > Warning: Could not determine atomic number from name [DY2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> > Warning: Could not determine atomic number from name [DX2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> > Warning: Could not determine atomic number from name [DZ1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> > Warning: Could not determine atomic number from name [DZ2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> > Warning: Could not determine atomic number from name [DX1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> > Warning: Could not determine atomic number from name [DY1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DY2 ]
> > Warning: Could not determine atomic number from name [DY2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DX2 ]
> > Warning: Could not determine atomic number from name [DX2 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ1 ]
> > Warning: Could not determine atomic number from name [DZ1 ]
> > Warning: Could not determine atomic number from mass (3.000000) [DZ2 ]
> > Warning: Could not determine atomic number from name [DZ2 ]
> > [trajin ../prod113TNP-with2ADP2MG.mdcrd]
> > [prod113TNP-with2ADP2MG.mdcrd] contains 2500 frames.
> > [trajin ../prod123TNP-with2ADP2MG.mdcrd]
> > [prod123TNP-with2ADP2MG.mdcrd] contains 2500 frames.
> > [autoimage]
> > AUTOIMAGE: To box center based on center of mass, anchor is first
> > molecule.
> > [trajout 3TNP-with2ADP2MG-prod-51-60ns.mdcrd netcdf]
> > [run]
> >
> >
> > How do I fix this issue? Any help would be greatly appreciated.
> >
> > Thanks,
> > Richard
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 05 2013 - 14:30:02 PDT
