[gmx-users] Generating topology with pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Sun May 9 00:44:19 CEST 2010

Moeed wrote:
> Dear Justin,
> 1- Unfortunately, I am having difficulty running the simple program 
> pdb2gmx with pdb file you sent me for Hexane.. I have in working 
> directory pdb file and rtp files:
> Hexane-PRODRG.pdb  rtp.pdb
> pdb2gmx -f Hexane-PRODRG.pdb -o Hexane.gro -p Hexane.top >& output.pdb2gmx
> output.pdb2gmx says:
> Opening library file /chem_soft/gromacs/share/gromacs/top/FF.dat

Don't redirect the output - pdb2gmx needs you to choose the force field 
interactively.  Otherwise, specify it using the -ff flag, otherwise nothing will 
ever happen.

> 2-can you please tell me why I need rtp file? previously I just created 
> pdb file and used x2top an dI had no rtp file...

These two tools function in entirely different ways.  Any structure that you 
process with pdb2gmx will only have its topology created if it is present in the 
appropriate .rtp file.  See the manual for more details.



> ****************************************************************************************Also 
> I have tried x2top comamnd: x2top -f Hexane-PRODRG.pdb -o Hexane.top 
> -alldih -ff oplsaa -name HEX


> Generating bonds from distances...
> atom 0

There is a bug in x2top (a known issue):




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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