> On Dec 13, 2014, at 9:13 AM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
>
> Dear all,
>
> I would like to save the topology of a single molecule of UREA in order to prepare a box of water at a different concentration to the 8M UREA BOX
> using Amber 12:
>
> tleap -f leaprc.ff10
> loadoff 8Mureabox.off
> loadamberparams frcmod.urea
> savepdb UREABOX UREABOX-tleap.pdb
>
> now when i rerun tleap and i try to load the same file : UREABOX-tleap.pdb
> i get the following error ..looks like the residue name URE is not defined
>
> Creating new UNIT for residue: URE sequence:
>
> am I need to load a library file for the single molecule ..I can not find it in : amber12/dat/leap/prep
> or amber12/dat/leap/lib
>
> any help on this
I’ve noticed this before. At one point, I actually generated a .lib or .mol2 file for URE to solve this problem, but I’m not sure what I did with it.
There is actually a fairly easy solution, though (I think). Save a topology file from the UREABOX unit in tleap, then use ParmEd to generate a OFF file from it. So, for example:
tleap -f tleap.in
--- tleap.in ---
source leaprc.ff10
loadOFF 8Mureabox.off
loadAmberParams frcmod.urea
saveAmberParm UREABOX ureabox.parm7 ureabox.rst7
quit
--- end ---
Then you can read that into ParmEd:
parmed.py -p ureabox.parm7 -i parmed.in
--- parmed.in ---
loadRestrt ureabox.rst7
# Get rid of waters since we only care about urea
strip :WAT
writeOFF urea.off
--- end ---
This urea.off file should hopefully do what you need.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Dec 13 2014 - 08:00:02 PST
