Dear Amber users,
Thanks for you previous reply .
My model consists of iron sulphur cluster as one residue .Each of iron atom
in the Fe4S4 cluster is bonded with organic moieties.
I have already done the geometry optimization of cluster using Gamess . Now
I made the connectivity of my cluster with other residues using xleap .This
I did after specifying connect0, connect1, connect2,
and connect3 in the cluster .
check FS4
Checking 'FS4'....
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
WARNING: The perturbed charge: -2.000000 is not zero.
Checking parameters for unit 'FS4'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 2
Unit is OK.
> check l.off
check: Argument #1 is type String must be of type: [unit molecule residue
atom]
usage: check <unit> [parmset]
> check l
Checking 'l'....
WARNING: There is a bond of 0.045292 angstroms between:
------- .R<S1 10>.A<C8 14> and .R<S1 10>.A<O2 17>
WARNING: There is a bond of 49.381530 angstroms between:
------- .R<Q2 2>.A<O1 12> and .R<R1 5>.A<C7 10>
WARNING: There is a bond of 36.657305 angstroms between:
------- .R<Q2 2>.A<O3 14> and .R<R1 6>.A<C7 10>
WARNING: There is a bond of 0.226015 angstroms between:
------- .R<S1 7>.A<C8 14> and .R<S1 7>.A<O2 17>
WARNING: There is a bond of 0.043989 angstroms between:
------- .R<S1 9>.A<C8 14> and .R<S1 9>.A<O2 17>
WARNING: There is a bond of 0.188672 angstroms between:
------- .R<S1 11>.A<C8 14> and .R<S1 11>.A<O2 17>
Warning: Close contact of 1.769163 angstroms between .R<S1 10>.A<O1 15> and
.R<S1 10>.A<O2 17>
Warning: Close contact of 0.424351 angstroms between .R<S1 4>.A<H5 12> and
.R<S1 4>.A<H8 13>
Warning: Close contact of 2.023823 angstroms between .R<S1 4>.A<H8 13> and
.R<R1 3>.A<H1 9>
Warning: Close contact of 0.427060 angstroms between .R<R1 3>.A<H8 11> and
.R<R1 3>.A<H6 12>
Warning: Close contact of 2.241739 angstroms between .R<R1 3>.A<H6 12> and
.R<Q2 2>.A<O1 12>
Warning: Close contact of 0.451924 angstroms between .R<Q2 2>.A<H1 2> and
.R<Q2 2>.A<H5 3>
Warning: Close contact of 1.580025 angstroms between .R<Q2 2>.A<H1 2> and
.R<T11 1>.A<H4 10>
Warning: Close contact of 2.226108 angstroms between .R<Q2 2>.A<H1 2> and
.R<T11 1>.A<O1 12>
Warning: Close contact of 2.086557 angstroms between .R<Q2 2>.A<H5 3> and
.R<T11 1>.A<H4 10>
Warning: Close contact of 2.161870 angstroms between .R<R1 5>.A<H3 6> and
.R<S1 11>.A<H5 12>
Warning: Close contact of 2.072058 angstroms between .R<S1 7>.A<O2 17> and
.R<S1 7>.A<O1 15>
Warning: Close contact of 1.767852 angstroms between .R<S1 9>.A<O2 17> and
.R<S1 9>.A<O1 15>
Warning: Close contact of 2.007237 angstroms between .R<S1 11>.A<O2 17> and
.R<S1 11>.A<O1 15>
Warning: Close contact of 2.223627 angstroms between .R<S1 11>.A<H7 16> and
.R<S1 11>.A<H3 8>
Checking parameters for unit 'l'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 20
Unit is OK.
In the above specified l.off is the library file for the organic moeity and
FS4 is the library file for the iron sulphur cluster .
The warnings are shown only after making the connectivity .I expect that
after minimization it will be ok , though I may be wrong here.
Can you suggest whether I can use two force fields i.e gaff and .ff99SB .
I shall really appreciate you suggestion in this .
Thanks and Regards'
Kirtana
On Thu, Aug 6, 2009 at 4:42 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Kirtana,
>
> > I am using gaff force field to generate the topology and parameter file
> > for
> > my model whuihc consists of Iron -sulphur cluster .
> > Can anybody tell me what atom type should I use for iron . I used FE as
>
> I would be VERY wary of using GAFF for iron sulphur clusters. This is way
> outside of what it was designed to do. I suggest checking the literature to
> see what others have done since I know numerous people have looked at such
> systems in the past.
>
> > > saveamberparm u dendron.inpcrd dendron.prmtop
> > Checking Unit.
> > WARNING: There is a bond of 89.489923 angstroms between:
> > ------- .R<T111 1>.A<S1 11> and .R<FS4 45>.A<FE3 3>
> > WARNING: There is a bond of 47.863802 angstroms between:
> > ------- .R<T111 12>.A<S1 11> and .R<FS4 45>.A<FE4 4>
> > WARNING: There is a bond of 12.355854 angstroms between:
> > ------- .R<T111 23>.A<S1 11> and .R<FS4 45>.A<FE1 2>
> > WARNING: The unperturbed charge of the unit: -1.996800 is not zero.
>
> Looks to me like missing TER cards or a messed up initial structure. Bonds
> of 89 angstroms are not good! You need to check your initial structure and
> bonding carefully.
>
> > -- ignoring the warnings.
> >
> > Building topology.
> > Building atom parameters.
> > For atom: .R<FS4 45>.A<FE1 1> Could not find type: FE
> > For atom: .R<FS4 45>.A<FE1 2> Could not find type: FE
> > For atom: .R<FS4 45>.A<FE3 3> Could not find type: FE
> > For atom: .R<FS4 45>.A<FE4 4> Could not find type: FE
> > Parameter file was not saved.
>
> You need to provide a frcmod file containing the parameters for Iron and
> probably for the sulphur as well. If you tried to use antechamber it
> probably quit with an error and never actually produced the files you need.
> I suggest looking for parameters in the literature.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
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Received on Wed Aug 19 2009 - 20:42:40 PDT
