[gmx-users] grompp problem

[Yang Ye]

Tom Lenaerts wrote:
>>
>> Good problem description, but what was your command line, the 
>> location of
>> these files you edited and the value of GMXRC? I'm surmising that 
>> gromacs
>> isn't finding the .atp you changed.
>>
>
> What is the GMXRC?
>
> Below a more complete description:
>
> I first copied the entire top folder of gromacs to my local directory.
> In the top-folder.  I added the PTR information to aminoacids.dat
>
> I added to ffG53a6.rtp this information (according to the manual this 
> is sufficient since the other things are optional)
>
> [ PTR ]
> [ atoms ]
>    O2P    OA    -1.099       1
>      P     P     1.162       1
>    O3P    OA    -1.099       1
>    O1P    OM    -0.786       1
>     OH    OA    -0.178       1
>     CZ    CB     0.077       2
>    CE2  CR61    -0.038       2
>    CD2  CR61    -0.039       2
>    CE1  CR61    -0.029       3
>    CD1  CR61    -0.029       3
>     CG    CB     0.002       3
>     CB   CH2     0.056       3
>     CA   CH1     0.184       4
>      C     C     0.436       4
>      O     O    -0.546       4
>      N    NL     0.835       4
>
> [ bonds ]
>    O2P    P
>      P  O3P
>      P  O1P
>      P   OH
>     OH   CZ
>     CZ  CE2
>     CZ  CE1
>    CE2  CD2
>    CD2   CG
>    CE1  CD1
>    CD1   CG
>     CG   CB
>     CB   CA
>     CA    C
>     CA    N
>      C    O
>
>
> I added to ffG53a6.atp the following lines
>
>
>    CB  12.0110  ;     carbon in phosphotyrosine
> CR61  13.0190  ;     carbon in ring of phosphotyrosine
Not only in atp, but also in bon and nb. nb is a bit easy, only LJ 
parameters. But for bon, you need to specify any bonded, angle, dihedral 
interaction that CB and CR61 have in your molecule.
>
>
>
> All this was required to generat the toplogy file for gromacs from the 
> pdb.
> The let the pdb2grm work i needed to set the GMXLIB to this new folder 
> and eeverything worked correctly.
>
> these are the command lines that I used until I reached the error:
>
> -bash-3.00$ export GMXLIB=/u/tlenaert/Gromacs/signal/sh2/with/top
> -bash-3.00$ pdb2gmx -ff G53a6 -f sh2_pep.pdb -o sh2_pep.gro -p 
> sh2_pep.top
> -bash-3.00$ editconf -bt cubic -f sh2_pep.gro -o sh2_pep.gro -c -d 0.9
> -bash-3.00$ genbox -cp sh2_pep.gro -cs spc216.gro -o sh2_pep_b4em.gro 
> -p sh2_pep.top
> -bash-3.00$ grompp -f em.mdp -c sh2_pep_b4em.gro -p sh2_pep.top -o 
> sh2_pep.tpr
>
>
> it then crashes here
>
>
>
>
> Tom
>
>
>
>
>
>
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