Vishal Agarwal wrote:
Dear Justin,
Thanks for replying. I guess it should be -O4 from the convention but
have to look more deeply to figure out that.
I am noticing a few more things in the ffG45a3.rtp, entries like +N in
the bonds and angles section. Since there is no atom type N in the
monomer, are these entries correct or another typo ?
Probably another typo, unless glucose suddenly contains nitrogen and no one
notified the scientific community :) I would again suggest modifying the .rtp
entry (in a local copy of the .rtp file), modeled after ffG53a6.rtp, since it
appears to be more reliable. There is no need to alter the [atoms] section, but
it appears some of the bonded directives need some work.
-Justin
Vishal
On Sun, Feb 7, 2010 at 1:18 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Vishal Agarwal wrote:
Dear Justin,
Thanks for replying.
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?
;;
Should they be exactly in the same order as the rtp entry ? The
atom type I specified is definitely according to the standard
convention of rtp entry. I am using G45a3 as the force field.
Not to my knowledge. As long as all of the expected atoms are
there, you shouldn't have a problem.
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?
;;
No I didnt 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.
;;
The problem I am having is where to modify my coordinate file.
The residue doesnot contain a atom type 'O'.
Another curious question I have is suppose if I have another
system where the a monomer uint say GLCA (specified in rtp) is
connected by a bridging atom say Carbon. Do I need to create a
new rtp entry for pdbgmx to work or is there a work around by
specifying that carbon as a separate residue ?
The problem comes from this line in ffG45a3.rtp:
[ impropers ]
; ai aj ak al gromos type
C1 O5 -O C2 gi_2
Clearly the force field is expecting to assign an improper around
carbon C1 using an "O" atom in a previous unit as a reference. I
think this may be a typo in the file. The ffG53a6.rtp file has this
line for the same improper:
C1 O5 O1 C2 gi_2
I think this is what was intended. I do not know why the anomeric
carbon would be using a previous residue as a reference for
assigning an improper. Perhaps this is a bug. Make a local copy of
ffG45a3.rtp and fix the line to make it look like the ffG53a6.rtp
entry. Please report back if this works; it may need to be fixed
for a future release.
-Justin
Again thanks for replying.
Best,
Vishal
-Justin
Your help is appreciated.
Thanks,
Vishal
On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[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]>>
<mailto:[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
<mailto:[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
<mailto:[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> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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***********************************************
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> <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 <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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