[gmx-users] Regarding Residue..

[Justin Lemkul]

On 3/8/17 6:18 AM, Dilip H N wrote:
> I have created a glycylglycine.pdb using avogadro software..and its residue
> are..
>
>  N   DGLY A
>
>  CA  DGLY A
>
>  C   DGLY A
>
>  O   DGLY A
>
>  HA1 DGLY A
>
>  HA2 DGLY A
>
>  H   DGLY A
>
>  HN  DGLY A
>
>  N   DGLY A
>
>  CA  DGLY A
>
>  C   DGLY A
>
>  O   DGLY A
>  HA1 DGLY A
>  HA2 DGLY A
>
>  H   DGLY A
>
>  OXT DGLY A
>
>  HO  DGLY A
>
> But i intended for charmm FF whr residues are written as
>
> [DGLY]
>   [ atoms ]
> 	    N   NH1   -0.470  0
> 	   HN     H    0.310  1
> 	   CA   CT2   -0.020  2
> 	  HA1   HB2    0.090  3
> 	  HA2   HB2    0.090  4
> 	    C     C    0.510  5
> 	    O     O   -0.510  6
>
> Hw can i correlate my .pdb file residue with charmmFF36 residue..??
>
> and in glycylglycine there are total of 17 atoms but in charmm FF thr
> are only 7 atomic residues described as shown..
>

They're different things.  Amino acids prefixed with "D" in CHARMM are D-amino 
acids, e.g. inverted C-alpha stereochemistry from those typically found in 
nature.  Thus, DGLY is not appropriate here (of course, glycine is not chiral, 
but we have a DGLY version for atom type consistency).

Glycylglycine is just Gly-Gly, so you don't need a special residue for it; 
glycine is already in every protein force field (and shouldn't be named DGLY, 
anyway).

> How can i solve this problem..?? wht does OXT,HO describe..?? to which atom..
>

Have you visualized the structure and labeled its atoms?  The first step in any 
simulation process is using your eyes :)  Then think about what the normal 
biochemistry of amino acids is.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================