Dear Ruchika,
Kindly refer to TUTORIAL B4: Simulating a pharmaceutical compound using
antechamber and the Generalized Amber Force Field.
<
http://ambermd.org/tutorials/basic/tutorial4b/index.htm>
Briefly it looks like you did not change the name of the ligand or the
residue named UNK in the complex file to the same name as in your ligand
file.
the tutorial explains the steps to change the names.
Ayesha
UM
On Thu, Dec 4, 2014 at 3:14 PM, Ruchika Bhat <ruchikabhat31.gmail.com>
wrote:
> Hi everyone,
>
> Please guide me why this error is occurring.
> All the steps before this command works well. Even the .top and .crd files
> for the ligand are built. Still for generating the docked protein's .top
> and .crd error is generated.
>
>
> saveamberparm m final.top final.crd
> Checking Unit.
> Building topology.
> Building atom parameters.
> For atom: .R<UNK 213>.A<C 1> Could not find type: c3
> For atom: .R<UNK 213>.A<H 2> Could not find type: h1
> For atom: .R<UNK 213>.A<H1 3> Could not find type: h1
> For atom: .R<UNK 213>.A<H2 4> Could not find type: h1
> For atom: .R<UNK 213>.A<O 5> Could not find type: os
> For atom: .R<UNK 213>.A<C1 6> Could not find type: ca
> For atom: .R<UNK 213>.A<C6 7> Could not find type: ca
> For atom: .R<UNK 213>.A<C5 8> Could not find type: ca
> For atom: .R<UNK 213>.A<H5 9> Could not find type: ha
> For atom: .R<UNK 213>.A<H6 10> Could not find type: ha
> For atom: .R<UNK 213>.A<C2 11> Could not find type: ca
> For atom: .R<UNK 213>.A<H3 12> Could not find type: ha
> For atom: .R<UNK 213>.A<C3 13> Could not find type: ca
> For atom: .R<UNK 213>.A<H4 14> Could not find type: ha
> For atom: .R<UNK 213>.A<C4 15> Could not find type: ca
> For atom: .R<UNK 213>.A<N 16> Could not find type: nh
> For atom: .R<UNK 213>.A<C10 17> Could not find type: c3
> For atom: .R<UNK 213>.A<C9 18> Could not find type: c3
> For atom: .R<UNK 213>.A<H11 19> Could not find type: h1
> For atom: .R<UNK 213>.A<H12 20> Could not find type: h1
> For atom: .R<UNK 213>.A<H13 21> Could not find type: h1
> For atom: .R<UNK 213>.A<H14 22> Could not find type: h1
> For atom: .R<UNK 213>.A<C7 23> Could not find type: c3
> For atom: .R<UNK 213>.A<H7 24> Could not find type: h1
> For atom: .R<UNK 213>.A<H8 25> Could not find type: h1
> For atom: .R<UNK 213>.A<C8 26> Could not find type: c3
> For atom: .R<UNK 213>.A<H9 27> Could not find type: h1
> For atom: .R<UNK 213>.A<H10 28> Could not find type: h1
> For atom: .R<UNK 213>.A<N1 29> Could not find type: nh
> For atom: .R<UNK 213>.A<C11 30> Could not find type: ca
> For atom: .R<UNK 213>.A<N4 31> Could not find type: nb
> For atom: .R<UNK 213>.A<C13 32> Could not find type: ca
> For atom: .R<UNK 213>.A<N3 33> Could not find type: nb
> For atom: .R<UNK 213>.A<N5 34> Could not find type: nh
> For atom: .R<UNK 213>.A<C14 35> Could not find type: c3
> For atom: .R<UNK 213>.A<C15 36> Could not find type: c3
> For atom: .R<UNK 213>.A<O1 37> Could not find type: os
> For atom: .R<UNK 213>.A<C16 38> Could not find type: c3
> For atom: .R<UNK 213>.A<C17 39> Could not find type: c3
> For atom: .R<UNK 213>.A<H21 40> Could not find type: h1
> For atom: .R<UNK 213>.A<H22 41> Could not find type: h1
> For atom: .R<UNK 213>.A<H19 42> Could not find type: h1
> For atom: .R<UNK 213>.A<H20 43> Could not find type: h1
> For atom: .R<UNK 213>.A<H17 44> Could not find type: h1
> For atom: .R<UNK 213>.A<H18 45> Could not find type: h1
> For atom: .R<UNK 213>.A<H15 46> Could not find type: h1
> For atom: .R<UNK 213>.A<H16 47> Could not find type: h1
> For atom: .R<UNK 213>.A<N2 48> Could not find type: nb
> For atom: .R<UNK 213>.A<C12 49> Could not find type: ca
> For atom: .R<UNK 213>.A<N6 50> Could not find type: nh
> For atom: .R<UNK 213>.A<H23 51> Could not find type: hn
> For atom: .R<UNK 213>.A<C18 52> Could not find type: c3
> For atom: .R<UNK 213>.A<H24 53> Could not find type: h1
> For atom: .R<UNK 213>.A<H25 54> Could not find type: h1
> For atom: .R<UNK 213>.A<C19 55> Could not find type: c3
> For atom: .R<UNK 213>.A<H26 56> Could not find type: hc
> For atom: .R<UNK 213>.A<H27 57> Could not find type: hc
> For atom: .R<UNK 213>.A<C20 58> Could not find type: ca
> For atom: .R<UNK 213>.A<C25 59> Could not find type: ca
> For atom: .R<UNK 213>.A<H30 60> Could not find type: ha
> For atom: .R<UNK 213>.A<C21 61> Could not find type: ca
> For atom: .R<UNK 213>.A<H28 62> Could not find type: ha
> For atom: .R<UNK 213>.A<C22 63> Could not find type: ca
> For atom: .R<UNK 213>.A<H29 64> Could not find type: ha
> For atom: .R<UNK 213>.A<C23 65> Could not find type: ca
> For atom: .R<UNK 213>.A<O3 66> Could not find type: os
> For atom: .R<UNK 213>.A<C27 67> Could not find type: c3
> For atom: .R<UNK 213>.A<H34 68> Could not find type: h1
> For atom: .R<UNK 213>.A<H35 69> Could not find type: h1
> For atom: .R<UNK 213>.A<H36 70> Could not find type: h1
> For atom: .R<UNK 213>.A<C24 71> Could not find type: ca
> For atom: .R<UNK 213>.A<O2 72> Could not find type: os
> For atom: .R<UNK 213>.A<C26 73> Could not find type: c3
> For atom: .R<UNK 213>.A<H31 74> Could not find type: h1
> For atom: .R<UNK 213>.A<H32 75> Could not find type: h1
> For atom: .R<UNK 213>.A<H33 76> Could not find type: h1
> Parameter file was not saved.
> >
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Received on Thu Dec 04 2014 - 04:00:02 PST
