[gmx-users] Residue id of capped peptide getting changed when adding molecules

[Justin Lemkul]

On 11/15/18 12:39 AM, Dilip.H.N wrote:
> Hi,
> I have a capped peptide (ACE-ALA-NME) and now when i add the other
> molecules through the command "gmx insert-molecules", the residue id of the
> capped peptide, which was 1 as:
>      1ACE    CH3
>      1ACE   HH31
>      1ACE   HH32
>      1ACE   HH33
>      1ACE      C
>      1ACE      O
>      1ALA      N
>      1ALA     HN
>      1ALA     CA
>      1ALA     HA
>      1ALA     CB
>      1ALA    HB1
>      1ALA    HB2
>      1ALA    HB3
>      1ALA      C
>      1ALA      O
>      1NME      N
>      1NME     HN
>      1NME    CH3
>      1NME   HH31
>      1NME   HH32
>      1NME   HH33
> gets changed to 1,2 and 3 as in:
>      1ACE    CH3
>      1ACE   HH31
>      1ACE   HH32
>      1ACE   HH33
>      1ACE      C
>      1ACE      O
>      2ALA      N
>      2ALA     HN
>      2ALA     CA
>      2ALA     HA
>      2ALA     CB
>      2ALA    HB1
>      2ALA    HB2
>      2ALA    HB3
>      2ALA      C
>      2ALA      O
>      3NME      N
>      3NME     HN
>      3NME    CH3
>      3NME   HH31
>      3NME   HH32
>      3NME   HH33
>      4XYZ     N1
>      4XYZ     N2
>      4XYZ     C1 and so on...
>
> 1] How can i prevent the residue id's from getting changed..??(or) retain
> their residue id's..?

Why do you need them to be the same? There should be no functional 
purpose as far as GROMACS is concerned.

> 2] Since when residue id's gets changed, it is treated as different
> chains/molecules and bonds between them are shown as
> "Warning) Unusual bond between residues: 1(none) and 2 (protein)
> Warning) Unusual bond between residues:  2 (protein) and 3 (none)" when
> viewed in VMD. causing a problem...

What "problem" is this causing? VMD does this all the time with species 
it doesn't recognize, but it still renders everything as normal. If you 
have problems with VMD, there's a different mailing list for that.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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