Thanks a lot/Jamie
On Tue, Aug 11, 2009 at 11:54 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Jamie Seyed wrote:
Hi Justin,
Is there any information on the gmx-website that explains how I
should do that? Does the tip means I should separate my original
structure and the groups that I attached to it??/ Many Thanks/Jamie
Please see the manual, section 4.6.2. I don't know what you mean by
separating your structure.
-Justin
On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Jamie Seyed wrote: > Dear Justin, > Thanks for your all valuable
comments. Actually I got these 2 notes: >
-----------------------------------------------------------------------------------
> > NOTE 1 [file topol.top, line unknown]: > The largest charge
group contains 24 atoms. > Since atoms only see each other
when the
centers of geometry of the charge > groups they belong to are
within
the cut-off distance, too large charge > groups can lead to
serious
cut-off artifacts. > For efficiency and accuracy, charge group
should consist of a few atoms. > For all-atom force fields
use: CH3,
CH2, CH, NH2, NH, OH, CO2, CO, etc. > > NOTE 2 [file md.mdp, line
unknown]: > You are using a plain Coulomb cut-off, which might
produce artifacts. > You might want to consider using PME
electrostatics. > >
------------------------------------------------- > > How I can
trust my results specially for first one?? Many Thanks/Jamie
> You
should define smaller charge groups. The tip given in the note is
useful. As for note 2, never use cut-off for electrostatics.
It is
not as reliable as PME. -Justin > > > On Mon, Aug 10, 2009 at
9:18
PM, Justin A. Lemkul > wrote: > > > > Jamie Seyed wrote: > >
The gro
file: > ------------------------- > GROtesk MACabre and
Sinister >
1836 > 12 C 1 1.311 1.563 0.994 > 12 C 2 1.220 1.635 1.079 >
12 C 3
1.092 1.565 1.081 > 12 C 4 1.108 1.449 0.996 > ......... > > 12 H
118 1.438 1.092 1.244 > 12 H 119 1.413 1.098 1.426 > 12 H 120
1.291
1.033 1.329 > 2SOL OW 121 0.569 1.275 1.165 > 2SOL HW1 122 0.476
1.268 1.128 > 2SOL HW2 123 0.580 1.364 1.209 > > ....... > >
572SOL
HW2 1833 2.024 1.991 2.158 > 573SOL OW 1834 2.290 2.286 2.382 >
573SOL HW1 1835 2.320 2.214 2.320 > 573SOL HW2 1836 2.251 2.246
2.465 > 2.64467 2.64467 2.64467 > >
----------------------------------------- > and itp-file: > >
----------------- > > ; Include forcefield parameters > > [
moleculetype ] > ; Name nrexcl > C60CH3 3 > > [ atoms ] > ;
nr type
resnr residue atom cgnr charge > mass typeB chargeB massB > 1
opls_145 1 C60CH3 C 1 0 > 12.011 ; qtot 0 > 2 opls_516 1
C60CH3 C 2
0 > 12.011 ; qtot 0 > ..... > > > 71 78 79 69 3 1.740000e+02
5.000000e+00 > 3.000000e+00 1.740000e+02 5.000000e+00
3.000000e+00 >
69 79 80 2 3 2.580000e+02 5.000000e+00 > 3.000000e+00
2.580000e+02
5.000000e+00 3.000000e+00 > > [ system ] > ; Name > C60CH3 > > [
molecules ] > ; Compound #mols > C60CH3 1 >
----------------------------------------------- > > Oh Ok now I
understand that I should remove only one of the > [molecule]
> > >
The [ system ] and [ molecules ] directives *only* belong in
the >
system .top, never in an .itp file. Remove both [ system ]
and [ >
molecules ] from the .itp, and list the appropriate molecules
in the
> [ molecules ] directive of the .top only. > > -Justin > >
sections in itp-file (right)?? > > Thanks a lot/ Please let
me know
if still something is > missing.../Thanks/Jamie > > > On Mon, Aug
10, 2009 at 8:42 PM, Justin A. Lemkul > > >> wrote: > > > > Jamie
Seyed wrote: > > First I put 1000, but after editconf and
genbox it
has been > changed to 572. I only have 1 part with SOL 572...
> > >
I'm thoroughly confused. There is no need to manually
manipulate >
these sections if you're allowing genbox, genion, etc to >
manipulate > them for you. Please post the following
information to
get a > resolution: > > 1. Your .top file > 2. Your molecule.itp
file (you can delete out lines in the atoms, > bonds, dihedrals
section so the file is not unnecessarily > long - I'm >
really just
interested in the other directives that may be > present) > >
-Justin > > On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul
> > >
> > >>> wrote: > > > > Jamie Seyed wrote: > > Hi Justin, > >
Thanks
again... . Actully I have a question: I > have 1836 > atoms >
(572
water and 1 molecule with 120 atoms). In top > of my >
file.gro > I
have 1836 and in topology in [molecules] I have > c60ch3 > 1;
and >
SOL 572 which means the same as above. So how I should >
change it >
to get rid of error...??/ > > > The above should be correct.
However, you then have > in your .top > you posted earlier: > > >
[molecules] > molecule 1 > SOL 1000 > > This section is
probably the
source of your problem. > Again, as I > said before, there should
only ever be one [ molecules ] > section in > the .top file.
Sounds
like you've got two. > > -Justin > > Thank you in
advance.../Jamie >
On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul > > > > >
>> > > >
> > >>>> wrote: > > > > Jamie Seyed wrote: > > Hi Justin, >
Oh yes.
I had a line that include ff again > and I > deleted that >
(is that
ok)? now I got a new error related to > "number of >
coordinates in
> > > That's more than OK, that's correct. As Mark > pointed
> out,
there > should only ever be one invocation of [ > defaults ]
in > a
topology. > > > coordinate file does not match topology..." I >
should fix this > one now!! Simple one to > fix. Figure out where
the duplicate or > missing > molecules are within the
topology. I'm
> guessing your > molecule.itp > was really a molecule.top,
complete with [ > defaults ], [ > system ], > and [ molecules ]
directive, right? None of these > should be > present > in an
.itp
file, only a .top. > > -Justin > > Thanks a lot/Jamie > > >
On Mon,
Aug 10, 2009 at 8:10 PM, Justin A. > Lemkul > > > > > >> > >
> > >
>>> > > > > >> > > > > > >>>>> wrote: > > > Can you post the
contents of > molecule.itp? The > first > #include for > the
force
field is likely not the problem; > you've probably >
#included > it
again in molecule.itp. > > -Justin > > Jamie Seyed wrote: > >
Dear
all, > I have a topology contains line as > below. I > do not >
understand > what is wrong with it that I get an > error >
----------- > Program grompp, Version 4.0.5 > Source Code file:
topio.c, line: 415 > Fatal error: > Syntax error-File
ffoplsaa.itp,
line 18 > last line read: > '[defaults]' > Invalid order for
directive defaults > -------------- > according to the page > >
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
> I do not have twice default > section... SO I > do not >
know >
exactly > which files I should check... It says > topology
and ff. >
Topology > that I am using in grompp is as > below and the >
ffoplsaa.itp has > only one default section... > Would you please
help me to solve > the problem. > topol.top: ------------- >
#include "ffoplsaa.itp" > #include "spce.itp" > #include
"molecule.itp" > [system] > fullerene in water > [molecules] >
molecule 1 > SOL 1000 > -------------------- > Many Thanks in
Advance and I > appreciate your > help/Jamie > > On Mon, Aug 10,
2009 at 5:46 PM, > Jamie Seyed > > > > > >> > > > > >>> > > >
> > >>
> > > > >>>> > > > > >> > > > > > >>> > > > >> > > > > >
>>>>>> > >
wrote: > > Dear Vitaly, > topol.top: ------------- > #include
"ffoplsaa.itp" > #include "spce.itp" > #include "c80ch3.itp" >
[system] > fullerene in water > [molecules] > C80CH3 1 > SOL
1000 >
-------------------- > my command is: > grompp -f md.mdp -c
f.gro -p
> topol.top > -o pr.tpr > -maxwarn 10 > Thank you for helping me
out to > solve the > problem/ > Regards/Jamie > On Mon, Aug
10, 2009
at > 5:39 PM, > Vitaly > V. Chaban > > > > > >> > > > > >>> >
> > >
> >> > > > > >>>> > > > > >> > > > > >>> > > > > > >> > > > >
>>>>>> wrote: > > Jamie, > > The idea is the same. Some >
directive
> is not > at its > place. I > cannot say > which is exactly
because I > don't see > all the > picture with > your > topology
file (+included files). > Write the > sequence of >
directives as >
they go in .top (+included > .itp) and > then > we will see >
what
sections > must be shifted or maybe just > swapped. > >
Vitaly > >
On Tue, Aug 11, 2009 at 12:34 > AM, Jamie > Seyed > > > >> >
> > >
>>> > > > > >> > > > > > >>>> > > > > > >> > > > > > >>> > >
> > >
>> > > > > > >>>>>> wrote: > > Hi Vitaly, > > When I add it
back, I
got > the old > error > > ----------- > > Program grompp, Version
4.0.5 > > Source Code file: topio.c, > line: 415 > > Fatal
error: >
> Syntax error-File > ffoplsaa.itp, > line 18 > > last line
read: >
> '[defaults]' > > Invalid order for > directive defaults > >
----------- > > Now do you have any idea??? I > appreciate >
your >
help/Jamie > > > > On Mon, Aug 10, 2009 at > 5:22 PM, > Jamie
Seyed
> > > > >> > > > > > >>> > > > >> > > > > > >>>> > > > > >>
> > > >
> >>> > > > >> > > > > > >>>>>> > > wrote: > >> > >> Hi
Vitaly, >
>> I did it because I read from > >> > >
http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
> >> that says: > >> "One solution is to simply > comment
out > (or
delete) > the lines > of code out > >> in the file where it is >
included > for the > second time > i.e., > ..". So if it is >
>> the
case I am going to > undo it > to see what > happens... > I
will >
let you know. > >> Thanks/Jamie > >> On Mon, Aug 10, 2009 at
> 5:05
PM, > Vitaly > V. Chaban > > > > >> > > > > >>> > > > > > >>
> > > >
>>>> > > > > >> > > > > >>> > > > > > >> > > > > >>>>>> > > > >>
wrote: > >>> > >>> Why did you comment out > [defaults] in >
ffoplsaa.itp? The > general idea > >>> is that the sections
in the >
resulting > topology file > (after > including > >>> #include's)
must be > placed in the > strict order. > > > > > >
------------------------------------------------------------------------
> > > > > _______________________________________________ >
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jalemkul[at]vt.edu <http://vt.edu/>
<http://vt.edu <http://vt.edu/>> > > > | (540) > > 231-9080 >
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jalemkul[at]vt.edu <http://vt.edu/>
<http://vt.edu <http://vt.edu/>> > | (540) > 231-9080 >
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<http://vt.edu <http://vt.edu/>> | (540) > 231-9080 >
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<http://vt.edu <http://vt.edu/>> | (540) 231-9080 >
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======================================== Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar Department of Biochemistry
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