Thank you for your response. How can I convert the restart (ncrst) and cpin
restart (cpin) file to abver24 compatible format?
On Tue, Aug 27, 2024 at 11:34 AM Vinicius Cruzeiro <
vcruzeiro.architecttherapeutics.com> wrote:
> There are likely formatting differences in the RST7 and CPREST files
> between Amber18 and Amber24. You would need to fix these in order for the
> restart to run smoothly. I would just restart your simulation again.
>
> I hope this helps,
> Best,
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Scientist II, Computational Chemistry
> Architect Therapeutics
> Twitter: .vwcruzeiro
> ------------------------------
> *From:* Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
> *Sent:* Monday, August 26, 2024 8:39 PM
> *To:* Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>
> *Cc:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Error to run constant pH replica exchange in
> explicit solvent in amber18
>
> I generate a new cpin and prmtop file using the following command.
> /home/srabani/Downloads/amber24/bin/cpinutil.py -p amber18.prmtop -o
> amber24.cpin -resnames HIP AS4 GL4 TYR LYS -op amber24.prmtop
> Now the run is running well. But It starts from 0 ns. But I already have
> 100 ns run. Is there any possibility to restart the run?
>
>
> On Tue, Aug 27, 2024 at 8:39 AM Dulal Mondal <
> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
> Thank you for your response. I have already completed 100 ns production
> run. If I use amber24 will I start from the beginning? Or is there any
> possible can I convert amber18 generated cpin (e.g. cpin.rep.032) to
> amber24 compatible cpin so that I can restart my simulation.
>
> On Tue, Aug 27, 2024 at 5:50 AM Vinicius Cruzeiro <
> vcruzeiro.architecttherapeutics.com> wrote:
>
> Hello Dulal,
>
> Could you please try running your simulation with Amber24 and let us know
> if you encounter any issues? Since you’re currently using Amber18,
> addressing any problems might be challenging at this point since Amber18
> was released several years ago. Additionally, when using Amber24, ensure
> you regenerate your CPIN file with cpinutils.py from Amber24.
>
> I hope this helps!
>
> Best regards,
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Scientist II, Computational Chemistry
> Architect Therapeutics
> Twitter: .vwcruzeiro
> ------------------------------
> *From:* Dulal Mondal via AMBER <amber.ambermd.org>
> *Sent:* Monday, August 26, 2024 10:16 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] Error to run constant pH replica exchange in explicit
> solvent in amber18
>
> Dear Experts,
>
> I run constant pH replica exchange in amber19 using pmemd.cuda.MPI. My
> titratable residue is 48 (less than 50). But I get the following error
> message.
> At line 167 of file constantph.F90 (unit = 23, file = '004/cpin.rep.032')
> Fortran runtime error: Index 1 out of range for namelist variable stateinf
>
> In the mdout file I see the following message.
> Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
> |reading charge increments from file: 009/cpin.rep.032
> I also upload the cpin
> file.
> Thanking you in advance
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Mon Aug 26 2024 - 23:30:02 PDT
