[gmx-users] error with changing pdb file

[Justin A. Lemkul]

ksm tprk wrote:
> Hello Justin,
> 
> I used ffgmx.n2t gromacs force field. and my topology file is:
> 
> 
> 
> ;
> ;       This is your include topology file
> ;       Generated by x2top
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"
> 
> [ moleculetype ]
> ; Name            nrexcl
> ICE                 3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass 
>  typeB    chargeB      massB
>      1          C      1    UNK      C      0          0     12.011     
>  C          0          0   ; qtot 0
>      2          C      1    UNK      C      1          0     12.011     
>  C          0          0   ; qtot 0
>      3          C      1    UNK      C      2
> .....
>  24          C      1    UNK      C     23          0     12.011      C 
>          0          0   ; qtot 0
>     25          N      1    UNK      N     24          0    14.0067     
>  N          0          0   ; qtot 0
>     26          C      1    UNK      C     25          0     12.011     
>  C          0          0   ; qtot 0
> ......
> 
> 
> Thank you helping me,

I can't keep trying to help you if you don't provide relevant information.  If 
you want free help, you have to make it easy for those trying to help you.  This 
topology snippet is not at all what I asked to see.  To be clear, please post 
the following information:

1. The lines from the topology specified in the grompp error messages (the line 
numbers are given in the error messages)
2. The coordinate file entries that correspond to the atoms on those lines.  It 
would be helpful to see the coordinate file that works, as well as the one that 
was modified that no longer works.

Going back to your very first post, the root of the problem is that there are 
not bonded parameters in the ffgmx force field to describe whatever changes you 
made.  Since you have yet to actually demonstrate what these changes were and 
how the affected the topology, there is no better help that anyone can provide.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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