Following are Leap log, and i have attached my pdf file for Tip5p.pdb water model.
FATAL: Atom .R<TIP 200>.A<H1 1> does not have a type.
FATAL: Atom .R<TIP 200>.A<O 2> does not have a type.
FATAL: Atom .R<TIP 200>.A<H2 3> does not have a type.
FATAL: Atom .R<TIP 200>.A<EP1 4> does not have a type.
FATAL: Atom .R<TIP 200>.A<EP2 5> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
Following is my water.inp file.
tolerance 2.0
filetype pdb
output system_new_pdb.pdb
structure Tip5p.pdb
number 200
inside box 0. 0. 0. 30. 30. 30.
end structure
Kindly find the attachment of my pdb file as well.
[
https://res-h3.public.cdn.office.net/assets/mail/file-icon/png/generic_16x16.png]Tip5p.pdb<
https://gisto365-my.sharepoint.com/:u:/g/personal/saqlainzafar_gm_gist_ac_kr/EWBYbXNq2YZJtFr_K9xT62UBzmJ4UXPjQ7XQTKTZcsGYmg>
________________________________
보낸 사람: David A Case <david.case.rutgers.edu>
보낸 날짜: 2023년 7월 26일 수요일 오후 11:11
받는 사람: Zafar,Muhammad Saqlain <saqlainzafar.gm.gist.ac.kr>; amber.ambermd.org <amber.ambermd.org>
제목: Re: [AMBER] TIP5P water model parameter files issue
On Tue, Jul 25, 2023, Zafar,Muhammad Saqlain wrote:
>
>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.
Please examine the leap.log file and tleap output carefully. There is
almost certainly a error message before what you quoted above that will
explain the problem.
....dac
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- application/octet-stream attachment: Tip5p.pdb
Received on Wed Jul 26 2023 - 07:30:03 PDT
