Thank you Ayesha. But I had changed the name to UNK and all the steps have
been performed succesfully except for the last saveamberparm step where the
generation of top n crd was supposed to take place.
The ligand file alone with UNK residue name was used to generate its top n
crd files. Those files were generated properly.
Please see if something else could be incorrect
On Thu, Dec 4, 2014 at 5:07 PM, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> 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 - 05:00:02 PST
