Respected Sir,<br><br>Greetings from Pawan.<br>Thanks for all your kind help and suggestions.<br>I will work on this and ask you if I have further doubts.<br>Is it fine if I use the perl code given in <a href="http://wiki.gromacs.org/membrane-simulations">wiki.gromacs.org/membrane-simulations</a> for solvation after the genbox step to remove extra waters from the hydrophobic part of the bilayer ?<br>
<br>Thanking you,<br><br>Yours sincerely,<br>Pawan<br><br><div class="gmail_quote">On Tue, Mar 31, 2009 at 5:31 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>
<br>
Pawan Kumar 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 class="im">
Respected Sir,<br>
<br>
Greetings from Pawan.<br></div><div class="im">
Thanks for all your suggestions.<br>
Is it possible to use the lipid.itp file from Tieleman sir's website in combination with GROMOS 96 force field without any modification ?<br>
</div></blockquote>
<br>
If you want to use lipid.itp without any modification, you are restricted to the ffgmx (deprecated!) force field. For Gromos96-lipid.itp combination, simply remove the ";; parameters for lipid-GROMOS interactions," as these nonbonded combinations are for ffgmx only. Otherwise, the nonbonded interactions (which now have consistent combination rules) should be generated correctly.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Is it fine if I use the Gromos/Berger force field combination for the system I am using ?<br>
</blockquote>
<br></div>
That is a decision you will have to make based on a thorough examination of the literature, and the benefits and criticisms of these particular force field parameters.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I am sorry to ask this but can you please help me with some information how to modify the lipid.itp file ?<br>
</blockquote>
<br></div>
That depends entirely upon what you want to do. If you want Gromos/Berger, I've already told you. If you want OPLS/modified Berger, search the archives for Chris Neale's posts on that topic.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
I will edit vdwradii.dat file as per your suggestion.<br>
<br>
<br>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br></div><div class="im">
On Tue, Mar 31, 2009 at 4:53 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>
Pawan Kumar wrote:<br>
<br>
Respected Sir,<br>
<br>
Greetings from Pawan.<br></div><div><div></div><div class="h5">
I have edited the lipid.itp file to add just one line extra " H<br>
atom from the opls_force_filed.itp " at the end of lipid<br>
interactions data and that works fine.<br>
I have done this after seeing the archives. It was given either<br>
I should change the file for sigma and epsilon values or else<br>
just add this line.<br>
I think I have done it correctly. If not please correct me.<br>
<br>
<br>
No, that is incorrect. You need to add the additional atom type as<br>
well as convert C6/C12 to sigma/epsilon. Otherwise, the calculated<br>
nonbonded interactions are meaningless. Read instructions carefully!<br>
<br>
Force fields have to be internally self-consistent, so using the<br>
parameters from OPLS with Berger lipids will give spurious results.<br>
The only proper combinations are Gromos/Berger or OPLS/converted<br>
Berger.<br>
<br>
<br>
I have removed the position restraints after the inflategro<br>
procedure.<br>
After that I did energy minimization using define = -DFLEXIBLE.<br>
I will change the temperature as per your suggestion.<br>
I thought before solvating if I do position restraint mdrun the<br>
lipids will compact more surrounding the protein.<br>
<br>
<br>
No, your system will probably explode due to unsatisfied charge<br>
interactions and hydrogen bonds. There is a substantial dipole in<br>
each lipid headgroup that can repel the lipids away from each other<br>
if it is not shielded.<br>
<br>
<br>
Thats the step when I got Lincs warnings and segmentation fault.<br>
Then I tried solvating the system using genbox step and<br>
spc216.gro as the solvent.<br>
But before doing the solvation step I copied the vdwradii.dat<br>
file into the working directory and increased the value for<br>
carbon to 0.5.<br>
But the result of this was " Segmentation fault " again. Can you<br>
please tell me why I get the " Segmentation fault " here in this<br>
step.<br>
The command used was : genbox -cp comp_em27.pdb -cs spc216.gro<br>
-o box.pdb -p topol.top<br>
<br>
<br>
Using a 0.5-nm radius for carbon will cause problems of excess<br>
memory consumption, or otherwise breaks the calculation. Use<br>
something more along the lines of 0.35 or 0.375, and manually delete<br>
out any stray waters in the hydrophobic core.<br>
<br>
-Justin<br>
<br>
<br>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br>
On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul<br>
<<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>><br></div></div><div><div></div><div class="h5">
<mailto:<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>
Justin A. Lemkul wrote:<br>
<br>
<br>
<br>
Pawan Kumar wrote:<br>
<br>
Respected Sir,<br>
<br>
Greetings from Pawan.<br>
I have used force constants of 100000 in position<br>
restraint<br>
.itp files for proteins as suggested in Dr. Tieleman' s<br>
webisite for Inflategro.<br>
The mdp files are :<br>
<br>
<br>
The .mdp files look reasonable enough, although I don't<br>
know why<br>
you are applying position restraints during EM. If it is for<br>
InflateGRO, that is fine, but once the system is<br>
assembled, you<br>
should remove the position restraints from the protein to<br>
minimize the system more.<br>
<br>
And are you sure you want 300K? DPPC will be in a gel<br>
phase at<br>
that temperature. If you want a more realistic fluid-phase<br>
model, you'll have to go above 315K (323K is common).<br>
<br>
<br>
One thing I just noticed. You don't have solvent in your<br>
position-restrained run? That could be a big problem if the<br>
lipid<br>
headgroups are strongly repelled from one another. Add solvent<br>
before doing anything other than EM.<br>
<br>
-Justin<br>
<br>
<br>
*Topology file :*<br>
; Include forcefield parameters<br>
#include "ffoplsaa.itp"<br>
#include "lipid.itp"<br>
#include "dppc.itp"<br>
<br>
<br>
This section should not work, as written. Have you modified<br>
lipid.itp according to Chris Neale's half-epsilon<br>
double-pairlist method? If not, what you've done makes no<br>
sense. The Berger lipid parameters distributed through<br>
Tieleman's site are designed for use with the Gromos force<br>
fields. They can be modified (search in the archives),<br>
but that<br>
can also be a source of error. Users who have made<br>
mistakes in<br>
the conversion have seen their systems explode.<br>
<br>
-Justin<br>
<br>
; Include chain topologies<br>
#include "topol_A.itp"<br>
#include "topol_B.itp"<br>
#include "topol_C.itp"<br>
<br>
;#ifdef POSRES<br>
;#include "lipid_posre.itp"<br>
;#endif<br>
<br>
; Include water topology<br>
#ifdef FLEX_SPC<br>
#include "flexspc.itp"<br>
#else<br>
#include "spc.itp"<br>
#endif<br>
<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
; Include generic topology for ions<br>
#include "ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
PROTEIN IN DPPC BILAYER<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
Protein_B 1<br>
Protein_C 1<br>
DPPC 926<br>
;SOL 23552<br>
<br>
Please help with some suggestions.<br>
<br>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br>
On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul<br>
<<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>><br>
<mailto:<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>>><br>
<mailto:<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>><br>
<mailto:<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>
Pawan Kumar wrote:<br>
<br>
Respected Sir,<br>
<br>
Greetings from Pawan.<br>
I did the Inflategro procedure for the POPC<br>
bilayer<br>
generated<br>
using genconf.<br>
It took around 26 compressions for coming near the<br>
initial area<br>
(just above it).<br>
The minimization were all converged to Fmax <<br>
1350.<br>
If I decrease the Fmax less than this I am getting<br>
machine<br>
precision.<br>
But when I proceeded with the final compressed<br>
structure for pr<br>
mdrun it gave lincs warnings and ended with<br>
segmentation fault.<br>
As an alternative to this bilayer I used the<br>
DPPC bilayer<br>
(pre-equilibrated) which is given in GMX-Benchmark<br>
distribution.<br>
I carried out the same steps of Inflategro. I used<br>
the cutoff of<br>
14 A in the inflation and compression step also.<br>
In this case the the Steepest Descents<br>
converged to<br>
Fmax < 1000<br>
in all the steps. The maximum force war never<br>
above 850.<br>
But when I did position restraint mdrun with<br>
the last<br>
compressed<br>
file I got Lincs warnings and Segementation fault<br>
after few<br>
steps (30 - 40 steps).<br>
Can you please help how to proceed ?<br>
<br>
<br>
If the minimization procedure is adequately finishing,<br>
then the<br>
problem comes from something you are doing. If<br>
you post<br>
your .mdp<br>
file, we may be able to see if there are any obvious<br>
mistakes.<br>
<br>
-Justin<br>
<br>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>><br>
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Virginia Tech<br>
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Virginia Tech<br>
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<br>
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========================================<br>
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Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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