[AMBER] 回复: non-bonded params

From: <201612095.mail.sdu.edu.cn>
Date: Sat, 03 Nov 2018 07:06:10 +0800

   Maybe you can try parmed for your case.
   Xparmed is also available to modify the prmtop file. For detail
   informations. Please read the mannual.
   Best regards

   -------- åå§é®ä»¶ --------
   ä¸»é¢:Re: [AMBER] non-bonded params
   å件人:hosein geraili
   æ¶ä»¶äºº:AMBER Mailing List

     Thank you for your help. I have another question that I would be grateful
     if somebody help.
     I need to change the angle values for all the angles in a ligand inside a
     protein. In the .frcmod file I only can change the values of atom types
     for example FE-S-FE, but If I need to have a different value for
     FE1-S1-FE2 and FE1-S2-FE2, it is not possible to implement it through
     frcmod. How can I do that? I tried to do it through .prmtop, but it is
     impossible, too.
     On Friday, October 26, 2018, 8:24:35 PM GMT+2, Matias Machado wrote:
     Dear Hosein,
     You can add those interactions at the LJEDIT section, which can be defined
     at the bottom of a parameter file (i.e. frcmod), see the following threat
     from the AMBER mailing list: [http://archive.ambermd.org/201807/0247.html]
     # Sections' order in parameter file
     Or you can patch the topology using Parmed (See Manual: in particular
     commands "addLJtype" and "changeLJPair"), but be aware of the difference
     in atom-type and vdW-type definition.
     Researcher at Biomolecular Simulations Lab.
     Institut Pasteur de Montevideo | Uruguay
     ----- Mensaje original -----
     De: "hosein geraili"
     Para: amber.ambermd.org
     Enviados: Viernes, 26 de Octubre 2018 13:30:36
     Asunto: [AMBER] non-bonded params
     Hi all,I need to use a scaling factor on the result of the
     Loerntz-Berthelot combination rule on two different atoms inside a
     protein. I found the force field files in the $AMBERHOME directory, but I
     don't know how to do this particular action. In Gromacs, I would add:
     [ nonbond_params ];i     j      func     Â
     Â sigma    epsilon O21    K      1   Â
     Â   number number
     in the ffnonbonded.itp, but I don't know how to do it in Amber.
     Any idea on how to do this?
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Received on Fri Nov 02 2018 - 16:30:02 PDT
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