[gmx-users] bond_atomtype

[Justin Lemkul]

On 5/2/16 4:53 AM, Ming Tang wrote:
> Dear list,
>
>
> I want to add parameters for silicon in oplsaa.ff
>
>
> In .rtp I added:
>
>
> [ SI ]
>   [ atoms ]
>      SI   opls_966   4.000     0
>
> In .atp I added:
>
>
>   opls_966   28.08000  ; Si++++
>
>
> In ffnonbonded.itp I added:
>
>
> opls_966   Si4+   14    28.08000     4.000       A    4.43500e-01  3.98000e-01
>
>
> In ions.itp I added:
>
>
> [ moleculetype ]
> ; molname   nrexcl
> SI          1
>
> [ atoms ]
> ; id    at type     res nr  residu name at name  cg nr  charge   mass
> 1       opls_966    1       SI          SI       1      4       28.0800
>
>
> when I run this comman:
>
> grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> I got this error:
> Unknown bond_atomtype SI
>
> Did I miss something or modify wrongly?
>

You have "Si4+" in ffnonbonded.itp and yet your bonded parameters probably refer 
to "SI."  The second column of ffnonbonded.itp (for OPLS-AA) determines the 
equivalent bonded type.  If that bonded type cannot be mapped back to a 
nonbonded type (first column of ffnonbonded.itp) you get an error.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================