[gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P
manik.mayur at gmail.com
Wed May 13 22:17:37 CEST 2009
On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul <jalemkul at 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.
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)
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.
>> 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.
>> Manik Mayur
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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