Vishal Agarwal wrote:
Dear Mark,
What I meant over here is the missing oxygen (-O) which pdbgmx
complains about is not a part of .rtp entry. There is no such type of
oxygen specified in any of the .atp entry of the forcefield I am using.
The "-O" is not an atom type, it indicates an oxygen atom of a previous residue.
It is still not clear what it is you're doing or what the actual problem is.
If you want a resolution, you'll have to do as Mark asked and post your command
line and the actual error message. Remember, you're asking for free help - you
have to make it easy for us to help you.
-Justin
Vishal
On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 07/02/10 14:52, Vishal Agarwal wrote:
Dear All,
Can anyone help me how can I go about preparing the topology
file for an
infinite crystal of cellulose. I have prepared the .gro file for
5X5X5
unit cells of cellulose II using GROMACS utility and intend to apply
periodic BC on it. It has a glucose molecule as building block
(GCLA).
When I try running pdbgmx, I get an error for extra hydrogens
(which is
not there in itp file but is actually there in the original
structure
which I am using) and missing oxygen (-O).
People who might help aren't at all interested in your description
of the error message. If the contents of your head were reliable,
you wouldn't have seen the error in the first place, or would have
solved the issue already. :-) Copy and paste your command line, and
what seems to be the relevant part of the error.
To use pdb2gmx, you need .rtp file entries that correspond to your
monomers. If not, you will not be able to use pdb2gmx to generate
your topology files.
Mark
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Regards
***********************************************
Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
***********************************************
'Your only obligation in any lifetime is to be true to yourself."
---Richard Bach
--
========================================
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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