Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine)

From: N.R. Jena <nrjena.gmail.com>
Date: Tue, 2 Mar 2010 22:29:38 +0530

Thank you very much Prof. Case. There was no error message. It was like:

{I am attaching herewith the .prepin and .frcmod files as well.}

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: OS - O2
Could not find bond parameter for: CK - P
Building angle parameters.
Could not find angle parameter: OS - O2 - P
Could not find angle parameter: CT - OS - O2
Could not find angle parameter: H5 - CK - P
Could not find angle parameter: CK - P - O2
Could not find angle parameter: CK - P - O2
Could not find angle parameter: CK - P - OS
Could not find angle parameter: NB - CK - P
Could not find angle parameter: N* - CK - P
Building proper torsion parameters.
 ** No torsion terms for OS-O2-P-O2
 ** No torsion terms for OS-O2-P-OS
 ** No torsion terms for CT-OS-O2-P
 ** No torsion terms for H5-CK-P-O2
 ** No torsion terms for H5-CK-P-O2
 ** No torsion terms for H5-CK-P-OS
 ** No torsion terms for NB-CK-P-O2
 ** No torsion terms for NB-CK-P-O2
 ** No torsion terms for NB-CK-P-OS
 ** No torsion terms for N*-CK-P-O2
 ** No torsion terms for N*-CK-P-O2
 ** No torsion terms for N*-CK-P-OS
Building improper torsion parameters.
old PREP-specified impropers:
 <6OG 7>: C4 C8 N9 C1'
 <6OG 7>: C5 N9 C4 N3
 <6OG 7>: N2 N3 C2 N1
 <6OG 7>: C2 H57 N2 H59
 <6OG 7>: C5 N1 C6 O6
 <6OG 7>: C6 C4 C5 N7
 <6OG 7>: H55 N9 C8 N7
 total 630 improper torsions applied
 7 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.



On Tue, Mar 2, 2010 at 6:41 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Mar 02, 2010, N.R. Jena wrote:
>
>> However, after fusing these
>> parameters .... I could not save proper .top and .crd
>> files for the whole DNA.
>
> Why not?  What commands did you use, and (most importantly): what was the
> error message?
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Tue Mar 02 2010 - 09:30:03 PST
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