Following are my commands to run tleap
packmol < water.inp &
tleap
source leaprc.protein.ff14SB
source leaprc.gaff
loadoff solvents.lib
HOH = TP5
WAT = TP5
loadamberparams frcmod.tip5p
mol=loadpdb system_new_pdb.pdb
setbox mol vdw
saveamberparm mol wtr_1.prmtop wtr_2.prmcrd
quit
While saving ( saveamberparm mol wtr_1.prmtop wtr_2.prmcrd ) following error comes.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
i want to know where i am having problem.
________________________________
보낸 사람: David A Case <david.case.rutgers.edu>
보낸 날짜: 2023년 7월 25일 화요일 오전 1:30
받는 사람: Zafar,Muhammad Saqlain <
saqlainzafar.gm.gist.ac.kr>; AMBER Mailing List <amber.ambermd.org>
제목: Re: [AMBER] TIP5P water model parameter files issue
On Mon, Jul 24, 2023, Zafar,Muhammad Saqlain via AMBER wrote:
>
>I need to use TIP5P water model to reproduce the density anomaly of water.
>
>but source leaprc.water.Tip5p and other parameter files are not found in my
>specified directory.
You can do this:
loadOff solvents.lib
HOH = TP5
WAT = TP5
That will load the TIP5P model, and make it the default for residues named
HOH or WAT. This will also load a TIP5PBOX unit that can be used in the
solvate commands in tleap. (To get pure water, solvate a TP5 unit).
I think(?) the reason we don't have a leaprc.water.tip5p file is that we
don't have recommended values for ions that go along with this model. But
if you just need a pure water simulation, what is in the solvents.lib file
should be what you need.
....good luck.....dac
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Received on Mon Jul 24 2023 - 23:00:03 PDT
