Re: [AMBER] addAtomType problem

From: Lea Natalia Toledo Carvajal <lea.toledo.pucv.cl>
Date: Fri, 8 Jul 2016 19:18:25 -0300

On Thu, Jun 30, 2016, Lea Natalia Toledo Carvajal wrote:

> 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.

To debug, you need to start slowly, with test cases: add a single new atom
type, building up the frcmod file one step at a time, and making sure that
each step works.

> addAtomTypes{{"Cu+2""Cu""sp3"}
{"Omu2""O""sp2"}}

You should certainly add spaces above, ...{"Cu2+" "Cu" "sp3"}.... But see
also below, since this the Cu2+ is a standard atom type.

> Could not find angle parameter: Cu+2 - Omu2 - Omu2

I think(!) this is because you have spaces in the Angle section of the
frcmod
file.

> For atom: .R<MOL 341>.A<CUP 1> Could not find vdW (or other)
> parameters for type: Cu+2

You are not adding libraries for metal ions. In AmberTools16, you need
to source leaprc.water.<type>, where <type> is the water model you want.
See the "Ions" section of the Reference Manual for more info.

Thanks Dac, these days I have been working on your suggestions, and seems
that tleap now recognises these new atoms types and its parameters
(attached as mix.txt file) But despite everything at the end of the process
the prmtop and inpcrd files are not written..
------------------------------------------------------------

 Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 38
Unit is OK.
Checking Unit.
WARNING: There is a bond of 3.416120 angstroms between:
------- .R<ALA 288>.A<C 9> and .R<GLY 289>.A<N 1>
WARNING: There is a bond of 3.078862 angstroms between:
------- .R<ARG 291>.A<C 23> and .R<ARG 292>.A<N 1>
WARNING: The unperturbed charge of the unit: -7.000000 is not zero.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
 ** No torsion terms for na-CU-Omu2-Omu2
 ** No torsion terms for NB-CU-Omu2-Omu2
 ** No torsion terms for CU-Omu2-Omu2-CU
Building improper torsion parameters.
 total 1127 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
*Parameter file was not saved.*
Writing pdb file: protein_tleap_prova.pdb
 Creating protein_tleap_prova.lib
Building topology.
Building atom parameters.
    Quit
-------------------------------------

As you can see in mix.frcmod file, these **No torsion terms** are present,
you can help me to understand what happens please?

Additionally, in the output of this last test are required new "improper
torsions" (attached as leap.txt), those in its majority correspond to the
tryptophan residue, which is not direct related (nor bonded) to the active
site that I pretend to describe. If tleap indicate that they are warnings
but not errors ┬┐Do you think that this could affect the parameter file
creation?

We have the v15 of Amber, but for this part I am working with the v14 of
AmberTools, as you can see in the log file. When tleap call the
frcmod.ff14SB ff file, atomic_ions.lib is one of the libraries that reads.
This library include the atom type CU2+ (charge 2.000) and the atom type CU
(charge 1.000) but accordingly to the published parameters for this type of
coordination the copper atoms has another charge , so I thought that the
best idea were define another type of copper, but suggestions are welcome.

Lea


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Received on Fri Jul 08 2016 - 15:30:02 PDT
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