Vishal Agarwal wrote:
Dear Justin,
I am trying to make topology file for cellulose II. The monomer unit is
glucose (residue type GLCA). I do the following:
pdb2gmx -f cellulose.gro
So then your "cellulose.gro" contains all the atoms of GLCA monomers, named
exactly as the force field expects them? Have you checked against the .rtp
entry? What force field are you using?
I am getting the following error while using pdbgmx.
"Fatal Error:
Atom -O not found in residue 2 while adding improper"
Atom type "O" is actually not part of the GLCA residue. Only atom type
OA is part of GLCA residue.
pdb2gmx is complaining about an atom, not an atom type. Somewhere in the .rtp
file (probably within the [impropers] section, there should be a line specifying
an atom named O that belongs to the preceding residue (hence the minus sign).
None of my .rtp files are like this. Did you create a custom .rtp entry?
Do I need to modify the rtp entry to suit my system or does this error
corresponds to something else ?
That will depend upon the answers to the above questions. If you created the
.rtp entry, then you'll have to fix the problem of naming mismatch. If you're
using the standard .rtp entry for the force field, then it's easier to modify
your coordinate file to match the naming expected by the force field.
-Justin
Your help is appreciated.
Thanks,
Vishal
On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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]>
<mailto:[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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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