[gmx-users] define a new residue

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jul 8 13:10:19 CEST 2012

Because I saw that residues defined in aminoacids.rtp file don't have H in their carboxyl and atom N. So I decided to remove H !


From: francesco oteri <francesco.oteri at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, July 8, 2012 3:28 PM
Subject: Re: [gmx-users] define a new residue

Why have you removed the hydrogen? 

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

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

Cordiali saluti, Dr.Oteri Francesco 

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