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.
-Justin
<snip>
****************************************************************************************Also
I have tried x2top comamnd: x2top -f Hexane-PRODRG.pdb -o Hexane.top
-alldih -ff oplsaa -name HEX
<snip>
Generating bonds from distances...
atom 0
There is a bug in x2top (a known issue):
http://www.gromacs.org/Documentation/Gromacs_Utilities/x2top
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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