Dear forum members
I try to incorporate two new atom types to the ff of Amber (Cu+2 and
Omu2) as David suggest , but the problem for to recognise their
associated parameters is unresolved.
I want to highlight that these atoms has the respective topology and
parameter files (Cup.lib/frcmod and o2.lib/frcmod).
The input for tleap is the next:
---------------------------------------------------------
log file: ./leap.log
source leaprc.ff14SB
source leaprc.gaff
addAtomTypes{{"Cu+2""Cu""sp3"}{"Omu2""O""sp2"}}
loadoff Cup.lib
loadoff o2.lib
loadoff cid.lib
loadoff hit.lib
loadamberparams mix.frcmod
x = loadpdb PPO_24jun.pdb
check x
saveamberparm x prmtop inpcrd
savepdb x protein_tleap_prova.pdb
saveoff x protein_tleap_prova.lib
quit
----------------------------------------------------------
Some lines from the ouput
---------------------------------------------------------
>> gaff = loadamberparams gaff.dat
Loading parameters: /home/lea/amber14//dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
>
> addAtomTypes{{"Cu+2""Cu""sp3"}{"Omu2""O""sp2"}}
> loadoff Cup.lib
Loading library: ./Cup.lib
..
...
...
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Cu+2 - Omu2 - Cu+2
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Cu+2 - Omu2 - Cu+2
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Omu2 - Cu+2 - Omu2
Could not find angle parameter: Omu2 - Cu+2 - Omu2
...
...
...
Building atom parameters.
For atom: .R<MOL 341>.A<CUP 1> Could not find vdW (or other)
parameters for type: Cu+2
For atom: .R<MOL 342>.A<CUP 1> Could not find vdW (or other)
parameters for type: Cu+2
For atom: .R<O2 343>.A<Omu2 1> Could not find vdW (or other)
parameters for type: Omu2
For atom: .R<O2 344>.A<Omu2 1> Could not find vdW (or other)
parameters for type: Omu2
Parameter file was not saved.
Thanks,
--
Lea Toledo
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Received on Thu Jun 30 2016 - 09:00:02 PDT
