[gmx-users] MD Simulation of DPPC Lipid Bilayer

[Justin A. Lemkul]

This is a bug that has been reported some time ago (by me).  To fix the issue, 
in the .rtp entry for [ NH2 ], change the improper line:

      N  H H  -C gi_1

to

      N  H1 H2  -C gi_1

-Justin

Nancy wrote:
> I tried to follow the "Membrane Protein" tutorial at:
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
> 
> I downloaded the "properly oriented" PDB file of the KALP-15 model peptide:
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/KALP-15_princ.pdb
> 
> I then attempted to run the pdb2gmx command:
> 
> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
> 
> For the force field, I chose #4, the "GROMOS96 53a6 force field", as 
> well as "None" for the termini, as stated in the tutorial.  However, 
> pdb2gmx outputs the following error message:
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: pgutil.c, line: 87
> 
> Fatal error:
> Atom H not found in residue 17 while adding improper
> -------------------------------------------------------
> 
> Please let me know how I should go about this.
> 
> Thanks,
> 
> Nancy
> 
> 
> 
> On Tue, Jul 28, 2009 at 1:12 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
>     Quoting Nancy <nancy5villa at gmail.com <mailto:nancy5villa at gmail.com>>:
> 
>      > Hello,
>      >
>      > I am new to Gromacs, but have prior experience with MD
>     simulations.  I'd
>      > like to setup and run a simulation of hydrated
>      > dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room
>     temperature
>      > (~298 K).  Are there tutorials that provide step-by-step
>     instructions on how
>      > to do this?
>      >
> 
>     Not directly, but there are several resources available.  Step 1 should
>     certainly be Chapter 5 of the manual, to understand how to construct the
>     topology of your system, since pdb2gmx will not do it for you.
>      Other than
>     that, there are general references online:
> 
>     http://oldwiki.gromacs.org/index.php/Membrane_Simulations
> 
>     There is also a plethora of question/answer threads in the list
>     archive, which
>     can be searched through the online interface:
> 
>     http://oldwww.gromacs.org/swish-e/search/search2.php
> 
>     Structures and topologies can be downloaded from a number of
>     research group
>     webpages, many of which are cited in the literature and mentioned in the
>     archived discussions.
> 
>     -Justin
> 
>      > Thank you.
>      >
>      > Nancy
>      >
> 
> 
> 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================