AMBER Archive (2009)

Subject: Re: [AMBER] Regd : gaff force field

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Fri Aug 07 2009 - 04:08:43 CDT

Hello Everyone,
You can simply remove the warnings and charge errors.
AMBER insert a space before the name of each heavy atom in the output
file. and most heavy atom names begin in column 14. and generally 2 two
heavy atoms FE(Iron) or CA (calcium) will not be correct. So you
should check the output file to edit it manually.
But regarding the warnings, you do one thing run the simulation with
cut=999, this will remove all such warnings. Do a minimization with
cut=999 initially and do your simulation from the resulting pdb file.

Ashish

On Fri, Aug 7, 2009 at 3:42 AM, KIRTANA S<skirtana4_at_gmail.com> wrote:
> 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_at_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_at_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.
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber