[gmx-users] H-atoms in .hdb file

[Shima Arasteh]

Oh, you're right. Those are the contents of the tdb file. I wrote hdb by mistake! sorry! :-)
Thanks so much Justin.


NOW,

1. I made an aminoacids.dat file and added FOR to other residues, as below:
49
ABU
ACE    
AIB
ALA  
ARG  
ARGN
ASN
ASN1  
ASP
ASP1
ASPH 
CYS 
CYS1
CYS2 
CYSH 
DALA
FOR
GLN  
GLU  
GLUH 
GLY
HIS 
HIS1
HISA 
HISB 
HISH 
HYP  
ILE  
LEU  
LYS  
LYSH 
MELEU
MET  
MEVAL
NAC  
NH2
PHE  
PHEH 
PHEU 
PHL 
PRO  
SER  
THR  
TRP  
TRPH 
TRPU 
TYR  
TYRH 
TYRU 
VAl


2. added FOR in .rtp file as before.


but now, it doesn't recognize the FOR as the first residue! My protein has 25 residue but here 24 is written by gromacs. What's the problem? .dat file defined is wrong?


 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, June 26, 2012 7:17 PM
Subject: Re: [gmx-users] H-atoms in .hdb file



On 6/26/12 10:44 AM, Shima Arasteh wrote:
>
>
> Thanks for you reply.
> As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb .
>
> In .rtp file:
>
>   [ atoms ]
>       C   CH1      0.380  0
>       O     O     -0.380  0
>   [ bonds ]
>       C      O
>       C     +N
>    [angles ]
>    ai    aj    ak
>    O     C     +N
>   [ dihedrals ]
>   O    C   +N   +CA
>
> In .n.hdb file:
>
>   [ replace ]
>       C   CH1      0.380  0
>       O     O     -0.380  0
>   [ bonds ]
>       C      O
>       C     +N

These are the contents of a .n.tdb file, as .n.hdb files do not exist.  You also
do not need such modifications.  If you have the formyl group in the .rtp file,
and it is appropriately defined as "Protein" in residuetypes.dat, then all you
need to do is choose "None" for the N-terminus of the protein.

>
> The first residue after formyl is VAL. I know when VAL is added to FOR, a peptide bond is formed and 1 H-atom is added to the N-atom in this bonding, this H-atom is already defined in .hdb file.
> In my case, an error ( missing H on VAL residue) is occured, thus I decieded to add the H by hand in pdb file.
>

The error probably comes from an incorrect assignment of terminus state.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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




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