Re: [AMBER] HPO4- and PO4-

From: Jones De Andrade via AMBER <amber.ambermd.org>
Date: Mon, 10 Feb 2025 15:39:19 -0300

Hi Gabriel.

I would have to check the gamess input, and also find an old script to
convert the dat file (you need to ensure that gamess is saving it
instead of deleting it from your scratch directory). I have a colleague
that most probably have them in a safe place.

On the other hand, I've never used antechamber for resp calculations:
Old school, hand-made inputs for the resp program itself.

I'm unsure if the new py_resp could possibly deal with gamess output
files.

What level of calculation are you using for it? Maybe there is another
way around it?

Best regards,

Jones 
---
Jones de Andrade
(jdandrade.iq.ufrgs.br)
DFQ/IQ/UFRGS
Lattes: http://lattes.cnpq.br/6675936210583999
Orcid: https://orcid.org/0000-0003-3429-8119
ResearcherID: https://publons.com/researcher/AAC-5337-2019/
Em 2025-02-10 15:24, Gabriel Ernesto Jara via AMBER escreveu:
> Hi Jones,
> 
> Thank you, II agree with you, for such as small molecule is better to
> calculate RESP charges.
> 
> I have no gaussian, so I optimized the molecule using GAMESS-US.
> However, I did not found much information about how to run ESP
> calculations and input it into antechamber.
> 
> The next GAMESS input, would be correct?
> 
> 
> """"""""
> 
>  $CONTRL SCFTYP=RHF EXETYP=RUN RUNTYP=OPTIMIZE COORD=UNIQUE $END
>  $CONTRL MOLPLT=.TRUE. $END
>  $STATPT NSTEP=100 $END
>  $BASIS  GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
>  $ELPOT  IEPOT=1 WHERE=PDC OUTPUT=PUNCH $END
>  $PDC    PTSEL=CONNOLLY $END
>  $GUESS  GUESS=HUCKEL $END
>  $DATA
> 
> """"""""""""""""''
> 
> If it is correct, how can use it in te antechamber command? just to
> include the option "-fi gamess"?
> 
> Can you help me?
> 
> Thank in advance
> 
> Gabriel
> 
> 
> ---
> Gabriel Ernesto Jara, PhD
> Specialist in Scientific Computation - JR.
> Brazilian Biosciences National Laboratory - LNBio
> Brazilian Center for Research in Energy and Materials -  CNPEM
> 10,000 Giuseppe Maximo Scolfaro St.
> Campinas, SP - Brazil 13083-100
> Phone: +55 19 3512-1255
> lnbio.cnpem.br/en
> ________________________________
> From: Jones de Andrade <jdandrade.iq.ufrgs.br>
> Sent: Friday, February 7, 2025 9:02 PM
> To: Gabriel Ernesto Jara <gabriel.jara.lnbio.cnpem.br>; AMBER Mailing
> List <amber.ambermd.org>; Gabriel Ernesto Jara via AMBER
> <amber.ambermd.org>; amber.ambermd.org <amber.ambermd.org>
> Subject: Re: [AMBER] HPO4- and PO4-
> 
> You don't often get email from jdandrade.iq.ufrgs.br. Learn why this
> is important<https://aka.ms/LearnAboutSenderIdentification>
> Hi.
> 
> If you allow my two cents here (at least concerning the charges): it
> is only a single one way too small molecule, and with a single minima
> conformation. The QM calculation will be way too cheap, and I wouldn't
> think twice before going to RESP.
> 
> The rest If the parametrization os a whole different matter, but I
> would still stick as much as possible to the standard amber protocol.
> 
> Best regards,
> 
> Jones
> 
> 
> Em 7 de fevereiro de 2025 13:56:44 BRT, Gabriel Ernesto Jara via AMBER
> <amber.ambermd.org> escreveu:
> 
> Dear all,
> 
> I want to parametrize the HPO4²⁻ ion. The ion is bound to a polarizing
> active site.
> 
> My questions area:
> 
>   *
> Is it recommendable to parametrize it using am1bcc charges and gaff2 ?
>   *
> or used am1bcc charges and modify the atom type to include the vdW
> radii
> (https://pubs-acs-org.ez106.periodicos.capes.gov.br/doi/10.1021/ct300613v)?
>   *
> or due to be highly charged, is better to calculate the RESP charges?
> 
> 
> Thank you in advance     
> 
> Gabriel
> ________________________________
> Gabriel Ernesto Jara, PhD
> Specialist in Scientific Computation - JR.
> Brazilian Biosciences National Laboratory - LNBio
> Brazilian Center for Research in Energy and Materials -  CNPEM
> 10,000 Giuseppe Maximo Scolfaro St.
> Campinas, SP - Brazil 13083-100
> Phone: +55 19 3512-1255
> lnbio.cnpem.br/en
> 
> 
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Received on Mon Feb 10 2025 - 11:00:03 PST
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