On Tue, Jun 28, 2016, Lea Natalia Toledo Carvajal wrote:
>
> I work in the setup of a metaloprotein (Cu+2), using the V.15 of AmberTools.
> For this system fortunately exist published the Amber parameters. But,
> when tleap read:
>
> > loadamberparams *.frcmod
>
> (file that include some of these special parameters), there are 3 that
> don't read.
You can use the "desc" command in tleap to see what has been loaded. Here
is what I get, when loading your file:
===========================================================================
> y = loadAmberParams example.frcmod
Loading parameters: ./example.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Unknown keyword: Cu+2-Omu2- in parameter file. Perhaps a format error?
Unknown keyword: Omu2-Cu+2- in parameter file. Perhaps a format error?
Unknown keyword: cc-na-Cu+2 in parameter file. Perhaps a format error?
Unknown keyword: c2-na-Cu+2 in parameter file. Perhaps a format error?
Unknown keyword: Cu+2-Omu2- in parameter file. Perhaps a format error?
Unknown keyword: Cu+2-Omu2- in parameter file. Perhaps a format error?
Unknown keyword: Omu2-Cu+2- in parameter file. Perhaps a format error?
> list
y
> desc y
PARMSET
--Atoms
--None
--Bonds
--None
--Angles
Cu+2 - NB - V Kt= 125.00 T0= 10.00 Desc:
NB - Cu+2 - na Kt= 109.50 T0= 0.01 Desc:
NB - Cu+2 - NB Kt= 109.50 T0= 0.01 Desc:
NB - Cu+2 - Omu2 Kt= 109.50 T0= 0.01 Desc:
CR - NB - Cu+2 Kt= 127.00 T0= 10.00 Desc:
O - C - n2 Kt= 80.00 T0= 122.90 Desc:
CX - C - n2 Kt= 70.00 T0= 116.60 Desc:
H - N - c Kt= 50.00 T0= 118.04 Desc:
CX - N - c Kt= 70.00 T0= 116.60 Desc:
O - C - n2 Kt= 80.00 T0= 122.90 Desc:
NB - Cu+2 - na Kt= 109.50 T0= 0.01 Desc:
Omu2 - Cu+2 - na Kt= 109.50 T0= 0.01 Desc:
--Torsions
--None
--Impropers
--None
--HBonds
--None
--Nonbonded Edits
--None
===========================================================================
So: do you see any "unknown keyword" errors? Have you entered (perhaps via
a leaprc file) the requisite AddAtomType commands (esp. for type Omu2)?
> Others similar warning message were solved adjusting the order of the
> alert with the sequence in which read the parameters in the *.frcmod
> file and work, but in this case this solution does not work.
I can't follow the above sentence: what does "adjust the order of the alert
with the sequence" mean--can you give an example?
Please try to provide a minimal example of a frcmod file that fails, and be
sure to give the *complete* set of commands that you gave to tleap.
...thanks...dac
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Received on Tue Jun 28 2016 - 07:30:02 PDT
