Thank you for your answer, this did help me.
Best,
Nora K.
Am Di., 11. Juni 2019 um 17:54 Uhr schrieb Matias Machado <
mmachado.pasteur.edu.uy>:
> Dear Nora Kremer,
>
> Your are missing the "!entry.URE.unit.connectivity" section in your .lib
> file, then atoms aren't connected or worst...
>
> The following lines do the magic...
>
> (AFTER !entry.URE.unit.connect)
>
> !entry.URE.unit.connectivity table int atom1x int atom2x int flags
> 1 2 1
> 1 3 1
> 3 4 1
> 3 5 1
> 6 1 1
> 6 7 1
> 6 8 1
>
> (BEFORE !entry.URE.unit.hierarchy)
>
> If you want to visualize the actual connectivity of your AMBER system in
> VMD, then don't load the PDB file... as connectivity information is
> normally absent in such format, VMD will guess about it, which means it may
> connect things just because they a close enough... as you are building the
> system from well defined molecules (with reasonable bond distances), then
> you may be hidden any connectivity issues...
>
> Instead, load the AMBER's topology and coordinates...
>
> vmd ure.prmtop -rst7 ure.rst
>
> Notice: topology must be named .prmtop for automatic detection, while I'm
> forcing VMD to read the ASCII AMBER format (rst7)
>
> Last but not least, some molecules split through PBC in the "test.pdb"
> file, that may not be the best initial setup for AMBER...
>
> Best,
>
> MatÃas
>
> PS: I don't know way people still uses the "old fashioned, heavy and
> restricted" ASCII format (.rst) instead of the "new fancy, light and
> flexible" NetCDF file format...
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Nora Kremer" <nora.kremer149.gmail.com>
> Para: amber.ambermd.org
> Enviados: Martes, 11 de Junio 2019 11:16:25
> Asunto: [AMBER] Urea water mixture
>
> Hello,
>
> I'm actually trying to build a water-urea mixture box with different urea
> concentrations.
> I'm generating .prm and .rst files in tleap using the following input:
> source leaprc.gaff
> source leaprc.water.tip3p
> loadamberparams frcmod.urea
> loadamberparams frcmod.ionsjc_tip3p
> loadoff urea_h.lib
> URE = loadpdb test.pdb
> set URE box { 22.336 22.336 23.445 }
> savepdb URE test_2.pdb
> saveamberparm URE ure.prm ure.rst
> The urea_h.lib (-> urea_h) is attached. I did this myself by loading one
> urea molecule into tleap and saving it as .lib file.
> The test.pdb file is generated by a self written program.
> Everything works fine, however, when saving the .prm and .rst files, I get
> following warnings:
> Warning: Unbonded Hydrogen atom H1 in URE.
> Cannot determine the requested GB radius for this atom.
> Writing the unmodified Bondi GB radius.
>
> Warning: Unbonded Hydrogen atom H2 in URE.
> Cannot determine the requested GB radius for this atom.
> Writing the unmodified Bondi GB radius.
> (I get this warning for all of the URE molecules)
>
> So it seems like there are no bonds. When visualizing the output pdb file
> in vmd, everything seems to be ok. However, when I try to start a
> minimization run, it doesn't even start. I used the min.in input with
> other
> systems, where it did work.
> So, I don't see where I made mistakes (in tleap perhaps ?) and I hope, that
> you can help me.
> (I'm using the Amber18 package.)
>
> Thank you
> Nora
>
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Received on Wed Jun 12 2019 - 07:30:04 PDT
