[gmx-users] Regarding Residue..

[Dilip H N]

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..

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

Can anybody kindly help regarding this ..


-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.



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