Hi Francesco,
Sorry for not responding...
> Beg pardon for the intrusion. Suppose you have modeled with DTF a
> tetrahedral complex of Zn(II), two aspartates, one HIS, and one H2O. The
> tetrahedral geometry is nearly perfect as it comes out from LEaP. However,
> on MD, Zn(II) and the three CA/O/O of the aas lie on a plane, with apical
> H2O. What would you conclude?
I would first carefully check if the topology generated by LEaP is
correct; I already observed a strange topology generated by LEaP once
in a similar case (a bug?); i.e. look at the prmtop/prmcrd files in
vmd for instance (removing the TIP3P molecules, but not the H2O-Zn one).
You can use 'rdparm prmtop' to read the prmtop file; then type bond,
angle or dihedral to read the FF parameters.
then, I would carefully check if the frcmod you generated is correct;
thus, are you sure the COO(-) groups bear the same atom types? for
instance I am not sure the frcmod provided below is advisable.
Finally, you could consider two cases (i) one with bonded parameters
and a non-integer partial charge for Zn2+ and (ii) without bonded
parameters and an integer (+2) charge value for Zn2+.
See
http://q4md-forcefieldtools.org/REDDB/Project/F-88/
> The DFT calculations were fine under every respect and the "bond" commands
> with LEaP were appropriate.
in the case (i) and if you use the mol2 file format output from R.E.D.
Server; you should not need to use the 'bond' command; the bonds
should be already defined.
> Looking at the distorted geometry with VMD, the
> bonds created with the "bond" commad are not seen, while the interatomic
> distances are correct for the required bonds, even after long MD
> simulation. I am not familiar enough with prm/crd to check there for bonds
> (which is an easy affair - for me - with psf)
looking at bonds in vmd is highly depend on the file format used;
better looking at the prmtop + boxcrd file; better not using the PDB
file format!
finally you could imagine to build a molecular system of the active
site only (i.e. without the protein; only with 3 dipeptides) and run
it in MD. do you get a similar deformation?
I hope this helps...
regards, Francois
> On Mon, Jun 3, 2013 at 4:51 PM, ros <rodrigogalindo.gmail.com> wrote:
>
>> Hello!
>> There are no parameters for copper atom (or any transition metal) in
>> the AMBER force fields. You have to load an external file with the
>> parameters for CU using the tleap command:
>>
>> loadamberparams copper.frcmod
>>
>> And in the copper.frcmod file something like:
>>
>> -----------------------------------------------------------------------------------------------------------------------
>> MASS
>> CU 63.55
>>
>> BOND
>> nb-CU 75.582 2.027
>> o-CU 84.879 1.907
>>
>> ANGLE
>> ha-ca-nb 52.970 116.000 same as ha-ca-n2
>> ca-nb-CU 50.523 114.913 from g09 calculations
>>
>> DIHE
>> ca-nb-cp-ca 1 4.800 180.000 2.000
>> ca-nb-cp-cp 1 4.800 180.000 2.000
>> nb-CU-nb-cp 1 14.800 180.000 2.000
>>
>> IMPROPER
>> o- o-CU-nb 1.1 180.0 2.0
>>
>> NONBON
>> CU 1.0330 0.0427 LJ parms from
>> http://dx.doi.org/10.1021/jp054177x
>>
>> -----------------------------------------------------------------------------------------------------------------------
>> This is an example of a file to add parameters for a molecule with
>> copper that I am working on. Do not use for your particular system!
>> You have to generate the parameters for your specific system and test
>> it with short MD runs to see if the geometry of the complex is
>> correct.
>>
>> Hope that helps a little!
>>
>> Rodrigo.
>>
>> On Mon, Jun 3, 2013 at 5:40 AM, Fabian Glaser <fglaser.technion.ac.il>
>> wrote:
>> > Hi,
>> >
>> > I am trying to prepare a protein for MD with amber, using for example
>> Maestro or Chimera. This protein has a Cu+2 atom. Once I have the partial
>> charges and hydrogens, I save the molecule in mol2 format but when I open
>> them with tleap for solvation, etc. it seems that the mol2 file is not read
>> properly so the atoms are not properly recognized.
>> >
>> > For example:
>> > (using default radius 1.500000 for CD1)
>> > (using default radius 1.500000 for CD2)
>> > (using default radius 1.500000 for CE1)
>> > (using default radius 1.500000 for CE2)
>> >
>> > (using default radius 1.500000 for OH)
>> > (using default radius 1.500000 for CU)
>> >
>> > I have also tried the opposite reading pdb directly, but in this case
>> the copper atom is not recognized:
>> >
>> > Unknown residue: CU number: 283 type: Terminal/last
>> >
>> > And then the charge is not correct.
>> >
>> > What is the right way to go?
>> >
>> > Thanks a lot,
>> >
>> > Fabian
>> > _______________________________
>> > Fabian Glaser, PhD
>> > Bioinformatics Knowledge Unit,
>> > The Lorry I. Lokey Interdisciplinary
>> > Center for Life Sciences and Engineering
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Received on Mon Jun 03 2013 - 23:30:03 PDT
