Hello Peter,<div><br></div><div>Thanks a lot for clarifying my doubt!</div><div>I have got it right now.</div><div><br></div><div>Thanks,</div><div><br></div><div>Anirban<br><br><div class="gmail_quote">On Thu, Dec 8, 2011 at 3:34 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;"><div class="im">On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote:<br>
> Hello Justin,<br>
><br>
> In your membrane protein simulation tutorial after making the topology, you have mentioned that "Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide." I suppose this is valid only for the proteins (and not membranes) to be processed through pdb2gmx using gromos53a6_lipid force-field, right? And to process a membrane using pdb2gmx we need to change the aminoacids.rtp file with the relevent POPC/DSPC/DPPC etc. entries. Right? Or can we somehow make pdb2gmx use the POPC/DPPC/DSPC.itp file?<br>
<br>
</div>Yes because in that tutorial, you are not adding an rtp with the lipid<br>
residue names to generate lipid topologies "from scratch". The tutorial<br>
uses pregenerated lipid topologies from Tieleman. You are certainly<br>
able to add your own rtp files; pdb2gmx searches all validly formatted<br>
rtp files in $GMXLIB/forcefield.ff/ for topology information by residue<br>
name. For example, when I converted parts of CGenFF to gromacs, I added<br>
my own library of residue types for the small molecules I am modeling as<br>
its own .rtp file. (Basically what I mean is, there is no need to hack<br>
aminoacids.rtp to add new residues, just add your own .rtp file).<br>
<br>
However you obtain a topology of a moleculetype (either using pdb2gmx or<br>
from someone else e.g. Tieleman) with a given forcefield, you do not need to<br>
run pdb2gmx again to generate another topology using that forcefield for<br>
subsequent tasks. Just include the relevant .itp file in the .top file<br>
you specify to grompp. For example, I generated POPC.itp once and have been<br>
using the same file for all my simulations involving POPC.<br>
<br>
Here is an entire membrane protein+lipid+water+ligand .top ready for<br>
grompp -p (I use charmm36 with cgenff added - this is analogous to Justin's<br>
gromos53a6_lipid modification):<br>
<br>
----<br>
#include "charmm36cgen.ff/forcefield.itp"<br>
#include "gpcr.itp"<br>
#include "popc.itp"<br>
#include "charmm36cgen.ff/tips3p.itp"<br>
#include "charmm36cgen.ff/ions.itp"<br>
#include "ligand.itp"<br>
<br>
[ system ]<br>
; Name<br>
GPCR in POPC with LIGAND<br>
<br>
[ molecules ]<br>
GPCR 1<br>
; the gpcr.itp file starts with:<br>
; [ moleculetype ]<br>
; ; Name nrexcl<br>
; GPCR 3<br>
POPC 230<br>
SOL 21468<br>
NA 2<br>
LIGAND 1<br>
----<br>
<br>
gpcr.itp, popc.itp, and ligand.itp were all originally generated by me using<br>
pdb2gmx on the relevant molecules coordinate files at one point or another.<br>
Again, these individual .itp files are reusable for other simulations<br>
involving the same molecule types, protonation states, and charmm36cgen.ff.<br>
<br>
Hope that helps.<br>
<br>
--<br>
==================================================================<br>
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>
(205) 690-0808 |<br>
==================================================================<br>
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