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
Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente.
Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.
________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 10 2025 - 10:30:02 PST
