Could you please let me know why such an error occurred even after loading
the frcmod file? I am attaching my pdb file here. The RNA is a single guide
RNA which is to be complexed with cas protein
On Mon, 7 Sep 2020 at 19:15, Jenny 148 <jenny.rs140.gmail.com> wrote:
> Sir,
> I have done the following in my system:
> loadamberparams GTP.frcmod
> source leaprc.RNA.OL3
> mol = loadpdb RNA.pdb
> saveamberparm mol rna.prmtop rna.inpcrd
>
> But I get the following error:
>
> FATAL: Atom .R<GTP 1205>.A<PA 1> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<PB 2> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<PG 3> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C5' 4> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O5' 5> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C4' 6> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O4' 7> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C3' 8> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O3' 9> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C2' 10> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O2' 11> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C1' 12> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<N1 13> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O1A 14> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O1B 15> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O1G 16> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C2 17> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<N2 18> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O2A 19> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O2B 20> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O2G 21> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<N3 22> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O3A 23> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O3B 24> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O3G 25> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C4 26> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C5 27> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C6 28> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<O6 29> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<N7 30> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<C8 31> does not have a type.
> FATAL: Atom .R<GTP 1205>.A<N9 32> does not have a type.
>
> Why does this happen?
>
> Jenny
>
>
>
> On Mon, 7 Sep 2020 at 18:02, David A Case <david.case.rutgers.edu> wrote:
>
>> On Mon, Sep 07, 2020, Jenny 148 wrote:
>> >
>> >I have a few systems of RNA- protein and DNA- protein complexes to work
>> >with. My RNA strands begin with a GTP and since I am a beginner, I do not
>> >know how to parametrize the GTP when it is in part of an RNA. Similarly,
>> I
>> >need to know how to include the 5' terminal phosphates of the DNA as
>> well.
>> >Could someone give some guidance regarding how to perform these tasks?
>>
>> If you have mono-phosphates at the 5' terminal ends of either DNA or RNA,
>> then use loadOff to lead terminal_monophosphate.lib after loading the
>> standard
>> leaprc files for DNA or RNA. (Your email wasn't clear about whether the
>> DNA
>> 5' phosphates were mono- or poly-phosphates).
>>
>> If you have a 5' GTP residue, you should be able to use the attached
>> files. These were derived from the stand-alone GTP residues prepared by
>> Heather Carlson and co-workers (see the contributed parameters database),
>> but modified to act as a 5' residue for RNA. Name the 5' residue "GTP"
>> in you input pdb file-- this is what the PDB itself does, but not all
>> PDB-like files follow this standard.
>>
>> ...good luck....dac
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
>
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- application/octet-stream attachment: RNA.pdb
Received on Mon Sep 07 2020 - 09:30:02 PDT
