Re: [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

[Justin A. Lemkul]

Manik Mayur wrote:
On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> 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.

-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


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    -- 
    ========================================

    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

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--
========================================

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

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