Yao Yao wrote:
Hi Justin,
Thanks for your last reply. Now it seems that OPLS has known the
atomtypes after I added those CA1, ... to ffoplsaanb.itp,
but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp,
it still gives errors like,
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
Opening library file
/share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
Generated 338253 of the 338253 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 338253 of the 338253 1-4 parameter combinations
ERROR 1 [file cro.top, line 37]:
No default Bond types
ERROR 2 [file cro.top, line 71]:
No default Angle types
ERROR 3 [file cro.top, line 72]:
No default Angle types
ERROR 4 [file cro.top, line 85]:
No default Angle types
ERROR 5 [file cro.top, line 91]:
No default Ryckaert-Bell. types
ERROR 6 [file cro.top, line 92]:
No default Ryckaert-Bell. types
ERROR 7 [file cro.top, line 93]:
No default Ryckaert-Bell. types
ERROR 8 [file cro.top, line 108]:
No default Ryckaert-Bell. types
ERROR 9 [file cro.top, line 112]:
No default Proper Dih. types
ERROR 10 [file cro.top, line 113]:
No default Proper Dih. types
ERROR 11 [file cro.top, line 114]:
No default Proper Dih. types
Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file cro.top, line 142]:
System has non-zero total charge: -1.022478e+00
This total charge suggests that your topology is badly broken.
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
There was 1 note
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986
Fatal error:
There were 11 errors in input file(s)
-----------------------------------------------
I do double-check those bondtypes, angles, and interactions mentioned in
the errors, and I am pretty sure I have already declared those values in
the ffoplsaabon.itp.
Is there any other file I also need to mention those values?
If these types were actually present in ffoplsaabon.itp, then you wouldn't get
these errors. Double check again.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
