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-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ################################################################## ----- Original Message ----- From: "kanika sharma" <ksharma997.gmail.com> To: "AMBER Mailing List" <amber.ambermd.org> Sent: Wednesday, November 6, 2013 3:13:05 PM Subject: Re: [AMBER] Fwd: Ligand has no type Hi, Am I the only who who cannot view the replies even after checking "receive mails in your email" button on mailing options? The reason I posted again is because I cannot find it anywhere on mailing list nor do I get email from user group. Thanks K.S On Wed, Nov 6, 2013 at 2:25 PM, Karl N. Kirschner < kkirsch.scai.fraunhofer.de> wrote: > Hello Kanika, > > I beleive both Jason Swails and David Case have responded to your > original email. Take a look at what they said, and follow their suggestions > about working through one of Amber's tutorials concerning nonstandard > molecules/residues. > > Best regards, > Karl > > ----- Original Message ----- > From: "kanika sharma" <ksharma997.gmail.com> > To: "AMBER Mailing List" <amber.ambermd.org> > Sent: Wednesday, November 6, 2013 2:19:36 PM > Subject: [AMBER] Fwd: Ligand has no type > > Hello Amber Users, > > Being fairly new at using Amber, I used a program for docking and got a > structure which I wanted to minimise and use further. I used leap as > instructions say and looked at the file that said: > > Loading PDB file: ./Taar131u19+CadaverineGoVina1.pdb > Unknown residue: LIG number: 341 type: Terminal/last > ..relaxing end constraints to try for a dbase match > -no luck > > Creating new UNIT for residue: LIG sequence: 342 > Created a new atom named: C1 within residue: .R<LIG 342> > Created a new atom named: C2 within residue: .R<LIG 342> > Created a new atom named: C3 within residue: .R<LIG 342> > Created a new atom named: N1 within residue: .R<LIG 342> > Created a new atom named: C4 within residue: .R<LIG 342> > Created a new atom named: C5 within residue: .R<LIG 342> > Created a new atom named: N2 within residue: .R<LIG 342> > total atoms in file: 2719 > Leap added 2723 missing atoms according to residue templates: > 2723 H / lone pairs > The file contained 7 atoms not in residue templates > Checking Unit. > WARNING: The unperturbed charge of the unit: -1.000000 is not zero. > FATAL: Atom .R<LIG 342>.A<C1 1> does not have a type. > FATAL: Atom .R<LIG 342>.A<C2 2> does not have a type. > FATAL: Atom .R<LIG 342>.A<C3 3> does not have a type. > FATAL: Atom .R<LIG 342>.A<N1 4> does not have a type. > FATAL: Atom .R<LIG 342>.A<C4 5> does not have a type. > FATAL: Atom .R<LIG 342>.A<C5 6> does not have a type. > FATAL: Atom .R<LIG 342>.A<N2 7> does not have a type. > Failed to generate parameters > Parameter file was not saved. > > How can I resolve this? Is it because I define ligand by LIG but then how > else should I define it? > > -- > *Regards,* > > *KS* > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 06 2013 - 07:00:03 PST