[gmx-users] aminoacids.n.tdb

Emine Deniz Tekin edeniztekin at gmail.com
Fri Apr 8 15:25:09 CEST 2011

Hi Gromacs users,

I want to covalently link the lauroic acid to the Valine residue (it is a
peptide (amide) bond), I know that I should update the specbond.dat.  But
before updating this file, I need the NH as an N terminal of the first
residue (Valine).  When I used  pdb2gmx with the –ter flag,  I got either
NH3, NH2 or None instead of NH. So, I add the [NH] directive in the
aminoacids.n.rtp file, as follows;

[ NH ]

[ replace ]

; old-name     new-type     new-mass      new-charge

         NL                N                14.0067           -0.31

        CA               CH1             13.019              0.127

[ add ]

1       2       H       N       CA      C

;atom_type      mass           charge

        H                 1.008          0.31

[ delete ]


[ bonds ]

N       H      gb_2

[ angles ]

CA      N       H      ga_11

[ dihedrals ]

H      N       CA      C       gd_29

(ps. I wrote the charges of N, CA and H according to values defined in
topol.top and also I used the Gromos96 53a6 force field)

Then, I used the pdb2gmx with –ter, I could see:

Select start terminus type for VAL

 0: NH

 1: NH3+

 2: NH2

 3: None

Finally, I got the  topol.top, posre itp and conf.gro files. But when I
looked into conf.gro,  I see that I am getting  “None”.  How can I get the
NH ?

Thanks in advance for your help.

Best regards

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