[email protected] wrote:
The problem seems to be between 3 S of CYS residues. I only use the 20 usual
residues and with no modifications.
An angle involving three S atoms? That should never occur.
Where is the ffbonded.itp file?
It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs
installation. If the problematic angle is indeed S-S-S, I guarantee you won't
find it there, though.
-Justin
Thank you,
Pierre THEVENET
----- Mail original -----
De: "Justin A. Lemkul" <[email protected]>
À: "Discussion list for GROMACS users" <[email protected]>
Envoyé: Mardi 17 Janvier 2012 15:12:58
Objet: Re: [gmx-users] grompp g96angle types error
[email protected] wrote:
Dear all,
I launch those commands for few models :
pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p
2it7-10_bestene1mc-SC.top -ignh -missing
editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0
-c -bt cubic
grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o
2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp
and at the grompp command I obtain :
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "2it7-10_bestene1mc-SC.top", line 1242]:
No default G96Angle types
Excluding 3 bonded neighbours for Protein 1
NOTE:
System has non-zero total charge: 1.000000e+00
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# G96BONDS: 254
# G96ANGLES: 367
# PDIHS: 149
# IDIHS: 108
# LJ14: 436
I don't understand the meaning of: No default G96Angle types.
All my files are generated by the same way, with the same softwares, and the
sames options. All the models are done by the same software so the .pdb file
only the coordinates of the protein change for one model to another.
Can you help me?
The error message indicates that angle parameters do not exist in the chosen
force field for a certain sequence of atoms. This would be highly unusual for a
standard protein. Are you using any custom residues? The error message
indicates the line in the .top that is causing the problem. Look it up, find
which atoms it corresponds to, and check ffbonded.itp to verify that suitable
parameters are indeed not present. If you're using some kind of custom residue
or nonstandard composition of atoms, then you'll likely have to parameterize the
missing term(s) yourself.
-Justin
--
========================================
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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