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
Received on Wed Nov 06 2013 - 06:30:03 PST
