On Thu, May 14, 2009 at 1:56 AM, Justin A. Lemkul <[email protected]> wrote:
> > > Manik Mayur wrote: > >> On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Manik Mayur wrote: >> >> Hi Users, >> >> I constructed a .pdb file for TIP4P water model which I tried to >> convert to .gro using pdb2gmx using: >> >> $ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p >> >> >> There is no need to use pdb2gmx. >> >> If you just need a TIP4P solvent box, one exists in the /share/top >> subdirectory of your Gromacs installation (tip4p.gro). >> >> >> 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. >> >> > OK, then that makes more sense. > > If you want to use your configuration, use editconf to convert it to >> .gro and #include "tip4p.itp" in your topology (which you can write >> by hand for a simple water system), or leave it as .pdb; Gromacs can >> use many different file formats for structures. >> >> >> yes, editconf will convert it to .gro but I was wondering why pdb2gmx is >> behaving in such unexpected manner? >> >> >> with the choice of forcefield as 5 (OPLS-AA/L all-atom force >> field). After conversion I found that the position of HW3(MW), >> the dummy atom is not the same relative to OW, what I kept in >> the .pdb file. Even during the conversion pdb2gmx gave warnings >> as "Warning: Long Bond (1773-1776 =....". >> >> >> What values does it find? (... does not help) >> >> >> e.g. >> Warning: Long Bond (8637-8640 = 8.73449 nm) >> .. and so on for many more pairs (all ~8 nm) >> >> Interestingly, if one runs pdb2gmx on the existing tip4p.gro that >> comes pre-installed, the program reports "Short bond" warnings. >> >> >> My .pdb file goes like this: >> ............ >> ATOM 1773 OW SOL 108 45.944 29.409 58.762 1.00 0.00 >> ATOM 1774 HW1 SOL 108 46.530 29.409 59.519 1.00 0.00 >> ATOM 1775 HW2 SOL 108 46.530 29.409 58.005 1.00 0.00 >> ATOM 1776 HW3 SOL 108 46.094 29.409 58.762 1.00 0.00 >> ............ >> note that the OW - HW3 is 0.15 angs as it should be. >> >> > 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. > Indeed the format was the issue, thanks for the help. -Justin > > So why is pdb2gmx recalculating the co-ordinates of HW3? How is >> the OW-HW3 bond is getting stretched? Also, what should be the >> correct procedure for the conversion? >> >> >> The residue name "SOL" is interpreted as "HOH," or a three-point >> water molecule. OPLS calls tip4p HO4 (per the .rtp file). This >> could be a potential source of error. >> >> >> with "-water tip4p" in pdb2gmx, SOL is interpreted as HO4, the default one >> however is HOH. >> >> Thanks, >> >> -Justin >> >> Thanks, >> >> Manik Mayur >> Graduate student >> Microfluidics Lab >> Dept. of Mechanical Engg. >> IIT Kharagpur >> INDIA >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> 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 >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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