Yes I want to simulate the protein inside DPPC bilayer but how could I make the index file. Everytime it is showing error that no DPPC found in index file.<br><br><div class="gmail_quote">On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Are you actually trying to simulate a membrane protein inside a DPPC bilayer<br>
though? If not, what is your reason for having it in your system?<br>
<br>
Also the topol.top file does not contain coordinates at all, only the<br>
forcefield parameterization.<br>
<div><div class="h5"><br>
On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote:<br>
> Please suggest me the exact way to include dppc coordinates in topol.top<br>
> file.<br>
><br>
> On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>wrote:<br>
><br>
> > On 1/02/2012 6:25 PM, Anushree Tripathi wrote:<br>
> ><br>
> > But in coordinate file(.pdb file) ,I am not getting the atoms which<br>
> > belongs to DPPC.<br>
> ><br>
> ><br>
> > You cannot do anything unless you have a coordinate file that includes<br>
> > DPPC coordinates. I don't know how to express this any more clearly.<br>
> ><br>
> ><br>
> > only I have included the name of dppc.itp file like this:<br>
> > ;Include DPPC chain topology<br>
> > #include "dppc.itp"<br>
> ><br>
> > That's why I have found the atoms wich belongs to DPPC molecule from<br>
> > dppc.itp file itself.<br>
> ><br>
> ><br>
> > These numbers are not useful, as I have already explained.<br>
> ><br>
> > Mark<br>
> ><br>
> ><br>
> ><br>
> ><br>
> > On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>wrote:<br>
> ><br>
> >> On 1/02/2012 6:04 PM, Anushree Tripathi wrote:<br>
> >><br>
> >> When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is<br>
> >> showing the following options:<br>
> >> 0 System : 18379 atoms<br>
> >> 1 Protein : 11739 atoms<br>
> >> 2 Protein-H : 9135 atoms<br>
> >> 3 C-alpha : 1173 atoms<br>
> >> 4 Backbone : 3519 atoms<br>
> >> 5 MainChain : 4693 atoms<br>
> >> 6 MainChain+Cb : 5773 atoms<br>
> >> 7 MainChain+H : 5842 atoms<br>
> >> 8 SideChain : 5897 atoms<br>
> >> 9 SideChain-H : 4442 atoms<br>
> >> 10 Prot-Masses : 11739 atoms<br>
> >> 11 non-Protein : 6640 atoms<br>
> >> 12 Water : 6636 atoms<br>
> >> 13 SOL : 6636 atoms<br>
> >> 14 non-Water : 11743 atoms<br>
> >> 15 Ion : 4 atoms<br>
> >> 16 CL : 4 atoms<br>
> >> 17 Water_and_ions : 6640 atoms<br>
> >><br>
> >><br>
> >> So your system has 18K atoms, with 11K protein and the rest solvent and<br>
> >> ions. As Justin suggested, this coordinate file does not have DPPC in it.<br>
> >><br>
> >><br>
> >><br>
> >> for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there<br>
> >> is no option for DPPC (as given in tutorial we have to merge protein with<br>
> >> DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n<br>
> >> index.ndx -o nvt.tpr),it is showing error:<br>
> >><br>
> >> Group DPPC not found in indexfile.<br>
> >> Maybe you have non-default goups in your mdp file, while not using the<br>
> >> '-n' option of grompp.<br>
> >> In that case use the '-n' option.<br>
> >><br>
> >> To troubleshoot the error,I have kept one more group in index.ndx file<br>
> >> with number of atoms which I found from dppc.itp file(at the end of file)<br>
> >> like this<br>
> >><br>
> >> [DPPC]<br>
> >> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15<br>
> >> 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30<br>
> >> 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45<br>
> >> 46 47 48 49 50<br>
> >><br>
> >><br>
> >> These numbers have to reference the atom numbers in the coordinate file,<br>
> >> not the [moleculetype]. Since you've done the latter, you get the problem<br>
> >> with T-coupling groups. But go back and use a coordinate file that actually<br>
> >> has DPPC in it.<br>
> >><br>
> >> Mark<br>
> >><br>
> >><br>
> >><br>
> >> Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p<br>
> >> topol.top -n index.ndx -o nvt.tpr),I am getting the following error:<br>
> >><br>
> >> Atom 1 in multiple T-Coupling groups (1 and 2).<br>
> >><br>
> >> Please suggest me the reason as well as solution for this problem.<br>
> >><br>
> >><br>
> >><br>
> >><br>
> >> --<br>
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</div></div>==================================================================<br>
<span class="HOEnZb"><font color="#888888">Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
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