[gmx-users] amber force field in gromacs

[Bruce D. Ray]

On Sat, November 21, 2009 at 2:36:08 AM, leila karami <karami.leila1 at gmail.com> wrote:

 
> I used amber03 force field in gromacs to study pr-dna interaction.
> I compare my pdb file and ffamber03.rtp file.
> I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1) and C-terminal
>  (NUMBER 70) of my protein is GLY.
> 
pdb file and rtp file relating to gly1 and gly70 are placed in follow.
> pdb file of gly1:
> 1  N  NGLY  1
> 2  CA NGLY  1
> 3  C  NGLY  1
> 4  O  NGLY  1
> 5 1H  NGLY  1
> 6 2HA NGLY  1
> 7 2H  NGLY  1
> 8 3H  NGLY  1
> 9 1HA NGLY  1
> rtp file of gly1:
> [ NGLY ]
>  [ atoms ]
>      N    amber99_39   0.29430     1
>     H1    amber99_17   0.16420     2
>     H2    amber99_17   0.16420     3
>     H3    amber99_17   0.16420     4
>     CA    amber99_11  -0.01000     5
> 
   HA1    amber99_28   0.08950     6
>    HA2    amber99_28   0.08950     7
>      C    amber99_2    0.61630     8
>      O    amber99_41  -0.57220     9
I could be wrong, but I believe that the atom names in the pdb file are supposed to match
the names in rtp entry.  There may be some formatting issues as well in your actual pdb file
since the error message references a residue GLY1 instead of residue NGLY1, but in the
absence of the actual pdb entry line, I cannot comment on that.


Sincerely


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091121/cf7391c6/attachment.html>