Prior to cat command, I parameterized and modify the naming schemes in my
pdb file in order for them to be consistent with AMBER. For the cat
command, I did the following command in terminal.
$cat 6DDE_PROA_3.pdb 6DDE_PROB_3.pdb 6DDE_PROC_3.pdb 6DDE_PROD_3.pdb
6DDE_PROE_3.pdb LIG.pdb BU72_Params/LIG.pdb 6DDE_MEMB_4.pdb >
6DDE_BU72_BMS_98612
This includes the 2 ligands I parameterized with antechamber and parmchk,
water and ions, the lipid bilayer, and individual protein chains.
I did not changed the atom names since then. I attached here the ligand
that cause the error in leap.
This is the other thing I do not understand, how can I say that the residue
name is unique? I am assuming that this is because I have 2 ligands
with residue name 'LIG'. Is this due to this naming style I did? Thank you
very much!
Best,
Mac Kevin E. Braza
On Thu, Dec 27, 2018 at 10:38 AM David Case <david.case.rutgers.edu> wrote:
> On Wed, Dec 26, 2018, Mac Kevin Braza wrote:
> >
> >I am preparing 2 ligands in complex with a GPCR in tLEaP after
> >parameterizing each component separately (i.e. antechamber, parmchk, and
> >tleap). However, whenever I combined them with cat command
>
> Can you give details here? What did you do *exactly* to "combine them
> with the cat command"?
>
> >* There are split residues;*
> >* residue sequence numbers will not correspond to those in the pdb.*
> >*-- residue 1253: duplicate [ C] atoms (total 15)*
> >*-- residue 1253: duplicate [ N] atoms (total 3)*
> >*-- residue 1253: duplicate [ O] atoms (total 2)*
> >*-- residue 1253: duplicate [Cl] atoms (total 2)*
>
> Please look carefully in your pdb file at residue 1253. Atom names
> within a residue must be unique (and must match exactly the atom names
> that antechamber used when you prepared the ligand.
>
> ....dac
>
>
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Received on Thu Dec 27 2018 - 03:00:01 PST
