[gmx-users] grompp g96angle types error
pithevenet at free.fr
pithevenet at free.fr
Tue Jan 17 15:38:32 CET 2012
Ok! The problem doesn't really come from gromacs so. It's my side-chain positioning software which made this... I'll try to fix it.
Thank you very much.
----- Mail original -----
De: "Justin A. Lemkul" <jalemkul at vt.edu>
À: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Envoyé: Mardi 17 Janvier 2012 15:30:08
Objet: Re: [gmx-users] grompp g96angle types error
pithevenet at free.fr 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.
> Thank you,
> Pierre THEVENET
> ----- Mail original -----
> De: "Justin A. Lemkul" <jalemkul at vt.edu>
> À: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Envoyé: Mardi 17 Janvier 2012 15:12:58
> Objet: Re: [gmx-users] grompp g96angle types error
> pithevenet at free.fr 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
>> 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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