Is there a reason specifically you want TIP5P? If your goal is simply to
have a water model that is better than TIP3P, would OPC work for you? This
is a 5-pt water model that does better than TIP5P in many respects. I'm
not sure about the density specifically but you can check out papers
from Onufriev's group on this. And lots of people use OPC in AMBER so the
parameter files are all set up for you.
On Thu, Jul 27, 2023 at 4:26 AM Zafar,Muhammad Saqlain via AMBER <
amber.ambermd.org> wrote:
> Thank you for your suggestion,
>
> I have tried to use Bond from frcmod.TIP3P file
>
> Bond
> OW-HW 553.0 0.9572
> HW-HW 553.0 1.5136
>
> But my error is constant same as before.
>
> 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.
>
> Is there any otherway i can do this ?
> ________________________________
> 보낸 사람: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> 보낸 날짜: 2023년 7월 27일 목요일 오전 12:25
> 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
>
> Hi,
>
> If you check by saving a TIP5P water (as pdb), you will see there is a
> triangulated portion consisting of OW and HW atoms (like in the TIP3P
> model). But, if you look at the frcmod.tip5p file, there is no mention of
> OW-HW and HW-HW bond parameters. These parameters are required for the
> successful building of your model system.
>
> If you create a frcmod file (in your working directory) by copying the
> bond parameters from the frcmod.tip3p file and supply its path in the tleap
> file before saving the topology and restart, the system can be built
> successfully. However, I don't know if it is a safe thing to do by just
> copying the other water parameters.
>
> With regards,
> Satyajit Khatua,
> Research Scholar,
> Department of Chemistry,
> IIT Kharagpur, Kharagpur-721302.
>
>
> On Wed, Jul 26, 2023 at 7:59 PM Zafar,Muhammad Saqlain via AMBER <
> amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
> 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://res-h3.public.cdn.office.net/assets/mail/file-icon/png/generic_16x16.png%5DTip5p.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<mailto:david.case.rutgers.edu
> >>
> 보낸 날짜: 2023년 7월 26일 수요일 오후 11:11
> 받는 사람: Zafar,Muhammad Saqlain <saqlainzafar.gm.gist.ac.kr<mailto:
> saqlainzafar.gm.gist.ac.kr>>; amber.ambermd.org<mailto:amber.ambermd.org>
> <amber.ambermd.org<mailto: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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Received on Thu Jul 27 2023 - 06:00:02 PDT
