[gmx-users] grompp problem

Tom Lenaerts tlenaert at vub.ac.be
Thu Mar 15 14:18:01 CET 2007

> 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

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  
-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  

it then crashes here


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