<br><br><br>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<br>
<br>Hi, Justin<br><br><br><br>grompp read the coordinate file : a6.gro from the output of editconf. editconf read the a6.gro ( output from the first pdb2gmx).<br><br>top file a6.top from the output of the first pdb2gmx.<br>
<br>I think the the coordinate file corresponds to the topology file a6.top.<br><br><br>Here is my command.<br><br> pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro<br><br> pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb<br>
<br> editconf -f a6.gro -o a6.gro -d 20.0<br><br> make_ndx -f a.pdb -o a6.ndx<br><br> grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr<br><br><br><br><br><div class="gmail_quote">On Mon, Feb 2, 2009 at 4:28 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
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.<br>
<br>
-Justin<br>
<br>
Liu Shiyong wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="Wj3C7c">
Hi, Justin<br>
I remove the del command. But I still got an error.<br>
<br>
make_ndx -f a.pdb -o a.ndx < make_ndx.input<br>
<br>
make_ndx.input:<br>
<br>
chain A and B& !a H*<br>
chain C& !a H*<br>
q<br>
<br>
<br>
<br>
checking input for internal consistency...<br>
Opening library file /export/apps/share/gromacs/top//ffG53a6.itp<br>
Opening library file /export/apps/share/gromacs/top//ffG53a6nb.itp<br>
Opening library file /export/apps/share/gromacs/top//ffG53a6bon.itp<br>
Opening library file /export/apps/share/gromacs/top//ff_dum.itp<br>
Generated 165 of the 1596 non-bonded parameter combinations<br>
Opening library file /export/apps/share/gromacs/top//spc.itp<br>
Opening library file /export/apps/share/gromacs/top//ions.itp<br>
Excluding 3 bonded neighbours molecule type 'Protein_A'<br>
Excluding 3 bonded neighbours molecule type 'Protein_B'<br>
Excluding 3 bonded neighbours molecule type 'Protein_C'<br>
<br>
NOTE 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]:<br>
System has non-zero total charge: -7.000002e+00<br>
<br>
<br>
<br>
processing coordinates...<br>
double-checking input for internal consistency...<br>
<br>
WARNING 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]:<br>
With nstlist=0 atoms are only put into the box at step 0, therefore<br>
drifting atoms might cause the simulation to crash.<br>
renumbering atomtypes...<br>
converting bonded parameters...<br>
initialising group options...<br>
processing index file...<br>
Making dummy/rest group for T-Coupling containing 4655 elements<br>
Making dummy/rest group for Acceleration containing 4655 elements<br>
Making dummy/rest group for Freeze containing 4655 elements<br>
Making dummy/rest group for Energy Mon. containing 1045 elements<br>
Making dummy/rest group for VCM containing 4655 elements<br>
Number of degrees of freedom in T-Coupling group rest is 13962.00<br>
Making dummy/rest group for User1 containing 4655 elements<br>
Making dummy/rest group for User2 containing 4655 elements<br>
Making dummy/rest group for XTC containing 4655 elements<br>
Making dummy/rest group for Or. Res. Fit containing 4655 elements<br>
Making dummy/rest group for QMMM containing 4655 elements<br>
T-Coupling has 1 element(s): rest<br>
Energy Mon. has 3 element(s): chAANDB_&_!H* chC_&_!H* rest<br>
Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>
User1 has 1 element(s): rest<br>
User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>
XTC has 1 element(s): rest<br>
Or. Res. Fit has 1 element(s): rest<br>
QMMM has 1 element(s): rest<br>
Checking consistency between energy and charge groups...<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.2<br>
Source code file: grompp.c, line: 150<br>
Fatal error:<br>
atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in different energy groups<br>
-------------------------------------------------------<br>
<br>
<br>
<br></div></div><div><div></div><div class="Wj3C7c">
On Fri, Jan 30, 2009 at 5:11 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Liu Shiyong wrote:<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.2<br>
Source code file: grompp.c, line: 150<br>
<br>
Fatal error:<br>
atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are<br>
in different energy groups<br>
-------------------------------------------------------<br>
<br>
<br>
Check your structure to make sure you are using the right coordinate<br>
file.<br>
<br>
Try to *not* delete every other group in the index file. Just<br>
because you don't need these groups in your energygrps does not mean<br>
they are not necessary for other functions.<br>
<br>
-Justin<br>
<br>
<br>
"Can someone please tell Icarus that he's not the only one<br>
falling from the sky?" (Urban Dance Squad)<br>
<br>
:-) G R O M A C S (-:<br>
<br>
GROningen Mixture of Alchemy and Childrens' Stories<br>
<br>
<br>
I checked the a.ndx<br>
<br>
[ System ]<br>
1 2 3 4 5 6 7 8 9 10 11 12 13<br>
14 15<br>
16 17 18 19 20 21 22 23 24 25 26 27 28<br>
29 30<br>
<br>
[ chAANDB_&_!H* ]<br>
1 5 6 7 8 9 10 11 12 14 15 16 17<br>
18 19<br>
23 24 25 26 27 28 29 30 31 32 34 35 36<br>
37 38<br>
<br>
[ chC_&_!H* ]<br>
2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587<br>
2588 2589<br>
2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605<br>
2606 2607<br>
<br>
<br>
<br>
-- Shiyong Liu<br>
Postdoc<br>
center for bioinformatics in the university of kansas<br>
Lab: (785)864-1962<br></div></div>
Email: <a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a><div class="Ih2E3d">
<br>
<mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>>> (<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a><br></div>
<mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>> <mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a><div class="Ih2E3d"><br>
<mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>>> or <a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a><br></div>
<mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>> <mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a><div class="Ih2E3d"><br>
<mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>>>)<br>
<br>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/~syliu</a><br></div>
<<a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/%7Esyliu</a>><div class="Ih2E3d"><br>
Lab: <a href="http://vakser.bioinformatics.ku.edu/people" target="_blank">http://vakser.bioinformatics.ku.edu/people</a><br>
Phone: (785) 864-1962<br>
<br>
<br>
------------------------------------------------------------------------<br>
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<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="Ih2E3d"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
<br>
<br>
<br>
-- <br>
Shiyong Liu<br>
Postdoc<br>
center for bioinformatics in the university of kansas<br>
Lab: (785)864-1962<br></div><div class="Ih2E3d">
Email: <a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a> <mailto:<a href="mailto:syliu@ku.edu" target="_blank">syliu@ku.edu</a>> (<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a> <mailto:<a href="mailto:shiyongliu@ku.edu" target="_blank">shiyongliu@ku.edu</a>> or <a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a> <mailto:<a href="mailto:liushiyong@ku.edu" target="_blank">liushiyong@ku.edu</a>>)<br>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" target="_blank">http://www.people.ku.edu/~syliu</a><br>
Lab: <a href="http://vakser.bioinformatics.ku.edu/people" target="_blank">http://vakser.bioinformatics.ku.edu/people</a><br>
Phone: (785) 864-1962<br>
</div></blockquote>
<br>
-- <br><div><div></div><div class="Wj3C7c">
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Postdoc<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone: (785) 864-1962<br>