Hello Dual,
You should disregard your Amber18 CPIN file and generate a new one using cpinutils.py from Amber24.
All the best,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: Dulal Mondal via AMBER <amber.ambermd.org>
Sent: Wednesday, September 4, 2024 7:06 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18
Dear Experts,
can anyone help me how I convert amber18 cpin file to amber24 cpin.
&CNSTPHE_LIMITS
NTRES= 71,
NTSTATES= 17,
NATCHRG= 315,
MAXH= 5,
/
This is for amber 24 cpin limits. How do I calculate NTSTATES, NATCHRG, MAX
from amber18 cpin file.
On Tue, Aug 27, 2024 at 11:43 AM Dulal Mondal <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> 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.*
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed Sep 04 2024 - 11:00:02 PDT
