AMBER Archive (2006)

Subject: Re[2]: AMBER: Could not find atom type.

From: Sergey Krishtal (skrishtal_at_mail.ru)
Date: Tue Apr 18 2006 - 05:48:07 CDT

Dear David and Yong,

Thank you very much for your help.

I've solved the problem with atom types: I've set explicitly the atom types after loading pdb file with command like below:
set ET1.1.C3 type C3

I would like to ask you some other questions that are probably rather silly ones but I'm not completely sure in these.

ET1 is ethanol molecule that I will use as a solvent for a some peptide. I've created a frcmod file which includes information about atom masses and non-bonded parameters. Ethanol molecule is supposed to be a rigid one with two united atoms: CH3 and CH2. When saving prmtop and inpcrd files Leap is complaining of missing parameters such as bond parameters, angle parameters, including ones for dyhedral angle. The first question is how can I specify the rigidity of ethanol molecule? Should I specify some force constants that will keep the geometry unchanged during simulation or is there another way to do this?
Second question is can I use FF03 all-atom force field along with my frcmod file containing molecule with united atoms?

Thanks in advance.

Best regards,
Sergey

On Mon, Apr 17, 2006, Sergey Krishtal wrote:
>
> Could you advise me please what to do in the following situation: I`m going
> to simulate CH2-group as a single site. I specified this group as C2. When I
> try to save prmtop and inpcrd files I get the following message: "Could not
> found type C2". However, leaprc.ff03 adds C2-type with sp3 hybridization.
>

We would need more details to know exactly what happened. But note that ff03
is an *all-atom* force field. Just because an atom is named "C2" does not
mean that you can use it to replace a CH2 group.

If you want a united atom force field, there is a new one in Amber 9, called
ff03ua.

....good luck....dac

 

-----Original Message-----
From: "Yong Duan" <duan_at_ucdavis.edu>
To: <amber_at_scripps.edu>
Date: Mon, 17 Apr 2006 09:45:10 -0700
Subject: RE: AMBER: Could not find atom type.

>
>
> Dear Sergey:
>
> You may check out this thread:
>
> http://amber.ch.ic.ac.uk/archive/200508/0081.html
>
> The error message means that the bond, bond angle, and torsion paramters for
> C2 type have not been defined/developed in AMBER (although the type has been
> defined). If you need the parameters, you may need to develop your own.
>
> It may be a good idea that you try antechamber to see the atom-type
> assignment which might be more compatible with AMBER ff parameter sets.
>
> yong
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of Sergey Krishtal
> > Sent: Monday, April 17, 2006 2:08 AM
> > To: amber_at_scripps.edu
> > Subject: AMBER: Could not find atom type.
> >
> >
> > Dear Amber Users,
> >
> > Could you advise me please what to do in the following
> > situation: I`m going to simulate CH2-group as a single site.
> > I specified this group as C2. When I try to save prmtop and
> > inpcrd files I get the following message: "Could not found
> > type C2". However, leaprc.ff03 adds C2-type with sp3 hybridization.
> >
> > I would be grateful for any help.
> >
> > Best regards,
> >
> > Sergey Krishtal
> >
>
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