Hi,
You should read carefully card 465 (missing residues, as well as other
cards in you pdb file), from that you must to add TER card after residues
358,465 and 534. From card ssbond (in you pdb file) replace CYS 402 and
CYS 423 to CYX residue. I did not check the RNA fragment.
Hope this will help you.
Hector.
> Dear All,
>
> I took a protein-RNA complex for MD studies. Then I separated protein and
> RNA since the purpose the the study is to compute the affinity between
> protein and RNA. Further I ran tleap using the script to combine the
> protein (File named as "rec1.pdb" in attachment) and RNA (File named as
> "rec2.pdb" in attachment) in AMBER12. After running the tleap script (File
> named as "tleap.all" in attachment), the followoing error was observed.
>
> Can you please help me to fix these errors
>
> Error
>
> Checking Unit.
> WARNING: There is a bond of 7.165783 angstroms between:
> ------- .R<LEU 358>.A<C 18> and .R<LYS 359>.A<N 1>
> WARNING: There is a bond of 7.638023 angstroms between:
> ------- .R<GLY 457>.A<C 6> and .R<SER 458>.A<N 1>
> WARNING: There is a bond of 7.123497 angstroms between:
> ------- .R<SER 520>.A<C 10> and .R<ASN 521>.A<N 1>
> WARNING: The unperturbed charge of the unit: 21.000000 is not zero.
>
>
> Could not find bond parameter for: SH - SH
> Building angle parameters.
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: CT - SH - SH
> Building proper torsion parameters.
> ** No torsion terms for HS-SH-SH-CT
> ** No torsion terms for HS-SH-SH-HS
> ** No torsion terms for CT-SH-SH-CT
> ** No torsion terms for CT-SH-SH-HS
> Building improper torsion parameters.
> total 843 improper torsions applied
>
> Checking Unit.
> WARNING: There is a bond of 15.809521 angstroms between:
> ------- .R<RU 204>.A<O3' 30> and .R<RC 205>.A<P 1>
> WARNING: The unperturbed charge of the unit: -46.000000 is not zero.
> FATAL: Atom .R<RG5 170>.A<P 33> does not have a type.
> FATAL: Atom .R<RG5 170>.A<OP1 34> does not have a type.
> FATAL: Atom .R<RG5 170>.A<OP2 35> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Checking Unit.
> WARNING: There is a bond of 7.123497 angstroms between:
> ------- .R<SER 520>.A<C 10> and .R<ASN 521>.A<N 1>
> WARNING: There is a bond of 7.638023 angstroms between:
> ------- .R<GLY 457>.A<C 6> and .R<SER 458>.A<N 1>
> WARNING: There is a bond of 7.165783 angstroms between:
> ------- .R<LEU 358>.A<C 18> and .R<LYS 359>.A<N 1>
> WARNING: There is a bond of 15.809521 angstroms between:
> ------- .R<RU 590>.A<O3' 30> and .R<RC 591>.A<P 1>
> WARNING: The unperturbed charge of the unit: -25.000000 is not zero.
> FATAL: Atom .R<RG5 556>.A<OP2 35> does not have a type.
> FATAL: Atom .R<RG5 556>.A<OP1 34> does not have a type.
> FATAL: Atom .R<RG5 556>.A<P 33> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
>
> Thanks & regards
>
> *Dr. Ramesh M*
> Email: shreeramesh.gmail.com
> Mobile: (91) + 9646469938 (27) + (0) 844556164
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
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Received on Mon May 11 2015 - 05:00:02 PDT
