[gmx-users] Regarding Residue in chain has different type (Other) from starting residue

[Dilip H N]

Thank you Justin Sir,

1] But how do i solve this issue..?? and make sure that pdb2gmx is not
interpreting my input as being a single chain and it's finding dissimilar
residue types..?? even i tried with gmx pdb2gmx with -ter command, but
still, i am getting the same results....

2] If i view the structure in VMD and type protein in Graphical
representations->selected atoms, I am viewing only Glycine, and if i type
resname TMAO then i am viewing the tmao molecules ..., any inference here
can i have here..??

Thank you...


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On Mon, Oct 16, 2017 at 1:30 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/15/17 2:42 AM, Dilip H N wrote:
>
>> Hello,
>> I have a simulations system and by gmx pdb2gmx i am generating the
>> topology, but i am getting the warnings as:-
>> Identified residue GLY1 as a starting terminus.
>> Warning: Residue TMAO12 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO13 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO14 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO15 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> Warning: Residue TMAO16 in chain has different type (Other) from starting
>> residue GLY1 (Protein).
>> More than 5 unidentified residues at end of chain - disabling further
>> warnings.
>> Identified residue GLY1 as a ending terminus....
>>
>> Topology is generated, but why am i getting this..?? all the parameters
>> for
>> tmao, glycine molecules are already prescribed in the .rtp, .atp
>> files etc., in forcefield...
>>
>> Any suggestions are appreciated...
>>
>>
>>
> It means pdb2gmx is interpreting your input as being a single chain and
> it's finding dissimilar residue types (something that's protein and other
> things that are not). There probably isn't any functional consequence to
> this, but pdb2gmx warns users about such cases because there are times when
> this can cause problems or unintended outcomes.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
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>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student