Liu Shiyong wrote:
pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p
r-l_365130_G53a6.minim_traj_withH_0.6.top -i
r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o
r-l_365130_G53a6.minim_traj_withH_0.6.gro
>r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 2>&1
Hi, Justin
grompp read the coordinate file : a6.gro from the output of editconf.
editconf read the a6.gro ( output from the first pdb2gmx).
top file a6.top from the output of the first pdb2gmx.
I think the the coordinate file corresponds to the topology file a6.top.
"Think" is not as definite as "know" - computers are literal, so you must be,
too.
Here is my command.
pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
Why are you running pdb2gmx twice? Unless you have multiple proteins, and need
multiple topologies, you should not be doing this.
editconf -f a6.gro -o a6.gro -d 20.0
You realize that the units of -d are nm, right? Do you need such a huge
solute-box distance?
make_ndx -f a.pdb -o a6.ndx
OK, here's the likely problem. If you're running pdb2gmx twice, you are
probably doing different things. So you're making an index file from a .pdb
file that was perhaps treated differently than the .gro file that corresponds to
a6.top. Use the .gro file as input into make_ndx and see if that alleviates the
problem.
grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
This *should* work, provided the .ndx file is what you actually think it is, and
you are using the correct topology.
-Justin
On Mon, Feb 2, 2009 at 4:28 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Alright, so how about the other comment I made? Are you using the
right coordinate file? I recall you got this error when you used
the non-pdb2gmx processed .pdb file as input into grompp. You must
use the coordinate file that corresponds to your topology.
-Justin
Liu Shiyong wrote:
Hi, Justin
I remove the del command. But I still got an error.
make_ndx -f a.pdb -o a.ndx < make_ndx.input
make_ndx.input:
chain A and B& !a H*
chain C& !a H*
q
checking input for internal consistency...
Opening library file /export/apps/share/gromacs/top//ffG53a6.itp
Opening library file /export/apps/share/gromacs/top//ffG53a6nb.itp
Opening library file /export/apps/share/gromacs/top//ffG53a6bon.itp
Opening library file /export/apps/share/gromacs/top//ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations
Opening library file /export/apps/share/gromacs/top//spc.itp
Opening library file /export/apps/share/gromacs/top//ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_B'
Excluding 3 bonded neighbours molecule type 'Protein_C'
NOTE 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]:
System has non-zero total charge: -7.000002e+00
processing coordinates...
double-checking input for internal consistency...
WARNING 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]:
With nstlist=0 atoms are only put into the box at step 0, therefore
drifting atoms might cause the simulation to crash.
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 4655 elements
Making dummy/rest group for Acceleration containing 4655 elements
Making dummy/rest group for Freeze containing 4655 elements
Making dummy/rest group for Energy Mon. containing 1045 elements
Making dummy/rest group for VCM containing 4655 elements
Number of degrees of freedom in T-Coupling group rest is 13962.00
Making dummy/rest group for User1 containing 4655 elements
Making dummy/rest group for User2 containing 4655 elements
Making dummy/rest group for XTC containing 4655 elements
Making dummy/rest group for Or. Res. Fit containing 4655 elements
Making dummy/rest group for QMMM containing 4655 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 3 element(s): chAANDB_&_!H* chC_&_!H* rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150
Fatal error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are
in different energy groups
-------------------------------------------------------
On Fri, Jan 30, 2009 at 5:11 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Liu Shiyong wrote:
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150
Fatal error:
atoms 1 and 2 in charge group 1 of molecule type
'Protein_A' are
in different energy groups
-------------------------------------------------------
Check your structure to make sure you are using the right
coordinate
file.
Try to *not* delete every other group in the index file. Just
because you don't need these groups in your energygrps does
not mean
they are not necessary for other functions.
-Justin
"Can someone please tell Icarus that he's not the only one
falling from the sky?" (Urban Dance Squad)
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens'
Stories
I checked the a.ndx
[ System ]
1 2 3 4 5 6 7 8 9 10 11
12 13
14 15
16 17 18 19 20 21 22 23 24 25 26
27 28
29 30
[ chAANDB_&_!H* ]
1 5 6 7 8 9 10 11 12 14 15
16 17
18 19
23 24 25 26 27 28 29 30 31 32 34
35 36
37 38
[ chC_&_!H* ]
2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585
2586 2587
2588 2589
2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601
2602 2605
2606 2607
-- Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu <mailto:sy...@ku.edu>
<mailto:sy...@ku.edu <mailto:sy...@ku.edu>> <mailto:sy...@ku.edu
<mailto:sy...@ku.edu>
<mailto:sy...@ku.edu <mailto:sy...@ku.edu>>>
(shiyong...@ku.edu <mailto:shiyong...@ku.edu>
<mailto:shiyong...@ku.edu <mailto:shiyong...@ku.edu>>
<mailto:shiyong...@ku.edu <mailto:shiyong...@ku.edu>
<mailto:shiyong...@ku.edu <mailto:shiyong...@ku.edu>>> or
liushiy...@ku.edu <mailto:liushiy...@ku.edu>
<mailto:liushiy...@ku.edu <mailto:liushiy...@ku.edu>>
<mailto:liushiy...@ku.edu <mailto:liushiy...@ku.edu>
<mailto:liushiy...@ku.edu <mailto:liushiy...@ku.edu>>>)
Homepage: http://www.people.ku.edu/~syliu
<http://www.people.ku.edu/%7Esyliu>
<http://www.people.ku.edu/%7Esyliu>
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
------------------------------------------------------------------------
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-- ========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu <mailto:sy...@ku.edu> <mailto:sy...@ku.edu
<mailto:sy...@ku.edu>> (shiyong...@ku.edu
<mailto:shiyong...@ku.edu> <mailto:shiyong...@ku.edu
<mailto:shiyong...@ku.edu>> or liushiy...@ku.edu
<mailto:liushiy...@ku.edu> <mailto:liushiy...@ku.edu
<mailto:liushiy...@ku.edu>>)
Homepage: http://www.people.ku.edu/~syliu
<http://www.people.ku.edu/%7Esyliu>
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu <mailto:sy...@ku.edu> (shiyong...@ku.edu
<mailto:shiyong...@ku.edu> or liushiy...@ku.edu <mailto:liushiy...@ku.edu>)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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