Dear Justin,<br><br>Thanks for replying. I really appreciate this.<br><br>Thanks,<br>Vishal<br><br><div class="gmail_quote">On Sun, Feb 7, 2010 at 3:58 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
<br>
Vishal Agarwal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin,<br>
<br><div class="im">
Thanks for replying. I guess it should be -O4 from the convention but have to look more deeply to figure out that.<br>
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 ?<br>
<br>
</div></blockquote>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Vishal<div><div></div><div class="h5"><br>
<br>
<br>
On Sun, Feb 7, 2010 at 1:18 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Vishal Agarwal wrote:<br>
<br>
Dear Justin,<br>
<br>
Thanks for replying.<br>
<br>
pdb2gmx -f cellulose.gro<br>
<br>
<br>
So then your "cellulose.gro" contains all the atoms of GLCA<br>
monomers, named exactly as the force field expects them?<br>
Have you<br>
checked against the .rtp entry? What force field are you using?<br>
<br>
;;<br>
<br>
Should they be exactly in the same order as the rtp entry ? The<br>
atom type I specified is definitely according to the standard<br>
convention of rtp entry. I am using G45a3 as the force field.<br>
<br>
<br>
Not to my knowledge. As long as all of the expected atoms are<br>
there, you shouldn't have a problem.<br>
<br>
<br>
<br>
I am getting the following error while using pdbgmx.<br>
<br>
"Fatal Error:<br>
Atom -O not found in residue 2 while adding improper"<br>
<br>
Atom type "O" is actually not part of the GLCA residue. Only<br>
atom type OA is part of GLCA residue.<br>
<br>
<br>
pdb2gmx is complaining about an atom, not an atom type.<br>
Somewhere<br>
in the .rtp file (probably within the [impropers] section, there<br>
should be a line specifying an atom named O that belongs to the<br>
preceding residue (hence the minus sign). None of my .rtp<br>
files are<br>
like this. Did you create a custom .rtp entry?<br>
<br>
;;<br>
No I didnt create a custom rtp entry.<br>
<br>
Do I need to modify the rtp entry to suit my system or<br>
does this<br>
error corresponds to something else ?<br>
<br>
<br>
That will depend upon the answers to the above questions. If you<br>
created the .rtp entry, then you'll have to fix the problem of<br>
naming mismatch. If you're using the standard .rtp entry for the<br>
force field, then it's easier to modify your coordinate file to<br>
match the naming expected by the force field.<br>
<br>
;;<br>
The problem I am having is where to modify my coordinate file.<br>
The residue doesnot contain a atom type 'O'.<br>
<br>
Another curious question I have is suppose if I have another<br>
system where the a monomer uint say GLCA (specified in rtp) is<br>
connected by a bridging atom say Carbon. Do I need to create a<br>
new rtp entry for pdbgmx to work or is there a work around by<br>
specifying that carbon as a separate residue ?<br>
<br>
<br>
The problem comes from this line in ffG45a3.rtp:<br>
<br>
[ impropers ]<br>
; ai aj ak al gromos type<br>
C1 O5 -O C2 gi_2<br>
<br>
Clearly the force field is expecting to assign an improper around<br>
carbon C1 using an "O" atom in a previous unit as a reference. I<br>
think this may be a typo in the file. The ffG53a6.rtp file has this<br>
line for the same improper:<br>
<br>
C1 O5 O1 C2 gi_2<br>
<br>
I think this is what was intended. I do not know why the anomeric<br>
carbon would be using a previous residue as a reference for<br>
assigning an improper. Perhaps this is a bug. Make a local copy of<br>
ffG45a3.rtp and fix the line to make it look like the ffG53a6.rtp<br>
entry. Please report back if this works; it may need to be fixed<br>
for a future release.<br>
<br>
-Justin<br>
<br>
<br>
Again thanks for replying.<br>
<br>
Best,<br>
Vishal<br>
<br>
-Justin<br>
<br>
Your help is appreciated.<br>
Thanks,<br>
Vishal<br>
<br>
On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>> wrote:<br>
<br>
<br>
<br>
Vishal Agarwal wrote:<br>
<br>
Dear Mark,<br>
<br>
What I meant over here is the missing oxygen (-O)<br>
which<br>
pdbgmx<br>
complains about is not a part of .rtp entry. There<br>
is no such<br>
type of oxygen specified in any of the .atp entry<br>
of the<br>
forcefield I am using.<br>
<br>
<br>
The "-O" is not an atom type, it indicates an oxygen<br>
atom of a<br>
previous residue. It is still not clear what it is you're<br>
doing or<br>
what the actual problem is. If you want a resolution,<br>
you'll<br>
have to<br>
do as Mark asked and post your command line and the<br>
actual error<br>
message. Remember, you're asking for free help - you<br>
have to<br>
make<br>
it easy for us to help you.<br>
<br>
-Justin<br>
<br>
Vishal<br>
<br>
<br>
On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
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<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>>>> wrote:<br>
<br>
On 07/02/10 14:52, Vishal Agarwal wrote:<br>
<br>
Dear All,<br>
<br>
Can anyone help me how can I go about preparing<br>
the topology<br>
file for an<br>
infinite crystal of cellulose. I have<br>
prepared the<br>
.gro<br>
file for<br>
5X5X5<br>
unit cells of cellulose II using GROMACS<br>
utility and<br>
intend to apply<br>
periodic BC on it. It has a glucose molecule as<br>
building<br>
block<br>
(GCLA).<br>
When I try running pdbgmx, I get an error for<br>
extra hydrogens<br>
(which is<br>
not there in itp file but is actually there<br>
in the<br>
original<br>
structure<br>
which I am using) and missing oxygen (-O).<br>
<br>
<br>
People who might help aren't at all interested<br>
in your<br>
description<br>
of the error message. If the contents of your head<br>
were reliable,<br>
you wouldn't have seen the error in the first<br>
place,<br>
or would<br>
have<br>
solved the issue already. :-) Copy and paste<br>
your command<br>
line, and<br>
what seems to be the relevant part of the error.<br>
<br>
To use pdb2gmx, you need .rtp file entries that<br>
correspond to<br>
your<br>
monomers. If not, you will not be able to use<br>
pdb2gmx<br>
to generate<br>
your topology files.<br>
<br>
Mark<br>
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-- Regards<br>
<br>
***********************************************<br>
Vishal Agarwal<br>
Research Scholar<br>
University of Massachusetts, Amherst<br>
***********************************************<br>
'Your only obligation in any lifetime is to be true to<br>
yourself."<br>
---Richard Bach<br>
<br>
<br>
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MILES-IGERT Trainee<br>
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Blacksburg, VA<br>
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***********************************************<br>
Vishal Agarwal<br>
Research Scholar<br>
University of Massachusetts, Amherst<br>
***********************************************<br>
'Your only obligation in any lifetime is to be true to<br>
yourself."<br>
---Richard Bach<br>
<br>
<br>
-- ========================================<br>
<br>
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ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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-- Regards<br>
<br>
***********************************************<br>
Vishal Agarwal<br>
Research Scholar<br>
University of Massachusetts, Amherst<br>
***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br>
---Richard Bach<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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-- <br>
Regards<br>
<br>
***********************************************<br>
Vishal Agarwal<br>
Research Scholar<br>
University of Massachusetts, Amherst<br>
***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br>
---Richard Bach<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Regards<br><br>***********************************************<br>Vishal Agarwal<br>Research Scholar<br>University of Massachusetts, Amherst<br>***********************************************<br>
'Your only obligation in any lifetime is to be true to yourself."<br> ---Richard Bach<br>