Hi Lea,
Obviously, your topology files miss some bonded and nonbonded parameters.
How 'd you created frcmod files for respective ligands? Your system looks
like part from ceruloplasmine. If so bonded strategy is to be applied. I do
not think that simple adding of atom types will solve the problem.
Cheers
Zoran
-----Original Message-----
From: Lea Natalia Toledo Carvajal
Sent: Thursday, June 30, 2016 5:58 PM
To: amber.ambermd.org
Subject: [AMBER] addAtomType problem
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 - 10:30:03 PDT
