[gmx-users] (no subject)

[Justin Lemkul]

On 3/25/13 2:37 AM, Emanuel Birru wrote:
> Hi Jeremy,
>
> I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how amber works well.
>

The directive is [dihedraltypes].  One can differentiate between propers and 
impropers by looking at the function type (see Table 5.5 in the manual).

> Another problem might be with your atom names ( CAD  OAX  CAB  CAG ) . If the atom names of your ligand are not available in the amber99sb ff, when you generate your top/itp file it wont understand them. If you want include new atom/molecule it is always good to get the parameters from some other literature or use the very similar kind of atoms to generate an itp and check whether your parameters are good or bad by calculating some other physicochemical property.
>

Atom names are not what ffbonded.itp uses.  Interaction types are defined by 
atom types.

-Justin

> By the way, you can include your atom/molecules or new parameters in general in amber99sb or any force field and generate you're an itp file for your new molecules. But you have to be careful not to mess up other parts of the ff. Or you can create your own copy and incorporate in the simulation package (top folder).
>
> It would be good if you explain what you are trying to do in detail to get more productive help.
>
> Cheers,
> EB
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yongliang Yang
> Sent: Monday, 25 March 2013 5:01 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] (no subject)
>
> Dear EB,
>
> Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, "No default proper dih. types'. Any advice?
> Thanks!
>
> Cheers
>
> Jeremy
>
>
>
> ---------------
> Hi Jeremy,
>
> I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section
>
> Yours look like
>    [ impropers ]
>    CAD  OAX  CAB  CAG       0.000   167.4 (two parameters here angle and
> force constant)
>
> Whereas the program is looking for
> CT  CT  OS  CT    9       0.0      1.60247     3  (here function, angel,
> force constant and multiplicity??) copied from the amber bonded force field parameter :)
>
> I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation.
>
> Cheers,
> EB
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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