<div class="gmail_quote">On Thu, May 14, 2009 at 1:56 AM, 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>
Manik Mayur wrote:<div class="im"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Thu, May 14, 2009 at 1:32 AM, 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>
Manik Mayur wrote:<br>
<br>
Hi Users,<br>
<br>
I constructed a .pdb file for TIP4P water model which I tried to<br>
convert to .gro using pdb2gmx using:<br>
<br>
$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p<br>
<br>
<br>
There is no need to use pdb2gmx.<br>
<br>
If you just need a TIP4P solvent box, one exists in the /share/top<br>
subdirectory of your Gromacs installation (tip4p.gro).<br>
<br>
<br>
Thanks for the reply. I needed to use pdb2gmx as it automatically checks for errors in the configuration file. Moreover apart from water, my system has silicon walls enclosing water.<br>
<br>
</blockquote>
<br></div>
OK, then that makes more sense.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
If you want to use your configuration, use editconf to convert it to<br>
.gro and #include "tip4p.itp" in your topology (which you can write<br>
by hand for a simple water system), or leave it as .pdb; Gromacs can<br>
use many different file formats for structures.<br>
<br>
<br>
yes, editconf will convert it to .gro but I was wondering why pdb2gmx is behaving in such unexpected manner?<br>
<br>
<br>
with the choice of forcefield as 5 (OPLS-AA/L all-atom force<br>
field). After conversion I found that the position of HW3(MW),<br>
the dummy atom is not the same relative to OW, what I kept in<br>
the .pdb file. Even during the conversion pdb2gmx gave warnings<br>
as "Warning: Long Bond (1773-1776 =....".<br>
<br>
<br>
What values does it find? (... does not help)<br>
<br>
<br>
e.g.<br>
Warning: Long Bond (8637-8640 = 8.73449 nm)<br>
.. and so on for many more pairs (all ~8 nm)<br>
<br>
Interestingly, if one runs pdb2gmx on the existing tip4p.gro that<br>
comes pre-installed, the program reports "Short bond" warnings.<br>
<br>
<br>
My .pdb file goes like this:<br>
............<br>
ATOM 1773 OW SOL 108 45.944 29.409 58.762 1.00 0.00<br>
ATOM 1774 HW1 SOL 108 46.530 29.409 59.519 1.00 0.00<br>
ATOM 1775 HW2 SOL 108 46.530 29.409 58.005 1.00 0.00<br>
ATOM 1776 HW3 SOL 108 46.094 29.409 58.762 1.00 0.00<br>
............<br>
note that the OW - HW3 is 0.15 angs as it should be.<br>
<br>
</blockquote>
<br></div>
The above is example is incorrect. You have an extra space between HW3 and SOL, which (when I run pdb2gmx on it), generates the long bond warnings. Check your .pdb file format and try again.<br>
</blockquote><br>Indeed the format was the issue, thanks for the help.<br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-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;"><div class="im">
So why is pdb2gmx recalculating the co-ordinates of HW3? How is<br>
the OW-HW3 bond is getting stretched? Also, what should be the<br>
correct procedure for the conversion?<br>
<br>
<br>
The residue name "SOL" is interpreted as "HOH," or a three-point<br>
water molecule. OPLS calls tip4p HO4 (per the .rtp file). This<br>
could be a potential source of error.<br>
<br>
<br>
with "-water tip4p" in pdb2gmx, SOL is interpreted as HO4, the default one however is HOH.<br>
<br>
Thanks,<br>
<br>
-Justin<br>
<br>
Thanks,<br>
<br>
Manik Mayur<br>
Graduate student<br>
Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>
IIT Kharagpur<br>
INDIA<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
<br>
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