chiloo777 777 wrote:
Do you mean i should change the order of #include thing in file.top or
something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
& popg.itp?
Without seeing your .top it's hard to give any really useful information. All
the bonded parameters for a given lipid should be included within the relevant
.itp file. If it's coming up as "not found" you're either using the wrong force
field, not #including something at all, or your topology is otherwise
incorrectly constructed.
-Justin
Thanks
Jit
On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham <[email protected]> wrote:
On 12/02/10 12:16, chiloo777 777 wrote:
Dear all,
I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"
-Before this process, i've changed the ffG53a6nb.itp& ff53Ga6bon.itp
according to the tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)
my topology, you can see the attached files.
Thanks in advance
Jit
--------------------------------------------------------------------------------------------
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations
ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
No default Proper Dih. types
If there's no default proper dihedral types defined, then you've #included
things in a wrong order.
Mark
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947
Fatal error:
Atomtype HO not found
-------------------------------------------------------
"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
--
========================================
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 [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
