[gmx-users] define a new residue

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jul 8 12:42:46 CEST 2012

Dear Francesco,
Thanks. Honestly I thought about this, but I don't know how much charges I need to increase or decrease of other atoms?

Is it possible to add the FVAL with the H atom( which I removed before)? I mean that I apply the complete formyl-valine and don't remove the H atom.

Thanks for your suggestions.


From: francesco oteri <francesco.oteri at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, July 8, 2012 3:04 PM
Subject: Re: [gmx-users] define a new residue

Hi Shima,
usually charge calculation are carried out on the system that is supposed to be used in the MD. 
So in my opinion you shouldn't remove the hydrogen. 
Anyway, if you wanna remove the hydrogen, either you increase the charge of some other atom or 
calculate the charges on the new residue without hydrogen.


2012/7/8 Shima Arasteh <shima_arasteh2001 at yahoo.com>

Hi dear gmx friends,
>I got the parameters of formyl-valine through the CHARMM website. Now I need to define it as a new residue FVAL( as Justin suggested me earlier) in .rtp file. To set the correct charges for atoms, I used the CHARMM output. In order to define FVAL to rtp file, I added these lines as below:
>CN    C    0.349    0
>    ON    O    -0.494    1
>    H1    HC    0.100    2
>    N    NH1    -0.423    3
>    HN    H    0.09    4
>    CA    CT1    0.144    5
>    HA    HB    0.09    6
>    CB    CT1    -0.097    7
>    HB    HA    0.09    8
>    CG1    CT3    -0.268    9
>    HG11    HA    0.09    10
>    HG12    HA    0.09    11
>    HG13    HA    0.09    12
>    CG2    CT3    -0.268    13
>    HG21    HA    0.09    14
>    HG22    HA    0.09    15
>    HG23    HA    0.09    16
>    C    C    0.209    17
>    O    O    -0.395    18
>As you see I omitted the H connected to Carboxyl. Now the total charge of the new-defined residue is not zero (-0.333) . How can I correct it?
>I would appreciate you for your suggestions.
>Thanks in advance.
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Cordiali saluti, Dr.Oteri Francesco

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