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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use thewww
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
