Different residues need different names, e.g. ALA != GLU.
Within a residue, different atoms need different names, e.g. C1 != C2,
we do not want two atoms named C.
Bill
On 12/27/18 2:58 AM, Mac Kevin Braza wrote:
> 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 - 04:30:02 PST
