[gmx-users] Capping residues

[Sai Pooja]

Thanks Marks. I tried it but this is what I get:

Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Do I need to edit the aminoacids.n.tdb file as well?

Pooja


On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- Original Message -----
> From: Sai Pooja <saipooja at gmail.com>
> Date: Friday, July 2, 2010 7:28
> Subject: Re: [gmx-users] Capping residues
> To: jalemkul at vt.edu, Discussion list for GROMACS users <
> gmx-users at gromacs.org>
>
> > I am sorry if I did not frame the question correctly, but putting it
> very simply, is there a way to use capping residues with the charmm
> forcefield if the residues are --COCH3 and NHCH3?
>
> Yes - you edit a copy of the .rtp file in your working directory and add
> whatever you want. Here's what I use in CHARMM
>
> [ ACE ]
>  [ atoms ]
>         CH3     CT3     -0.270  0
>         HH31    HA      0.090   0
>         HH32    HA      0.090   0
>         HH33    HA      0.090   0
>         C       C       0.510   1
>         O       O       -0.510  1
>  [ bonds ]
>         C       CH3
>         C       +N
>         CH3     HH31
>         CH3     HH32
>         CH3     HH33
>         O       C
>  [ impropers ]
>         C       CH3     +N      O
>
> [ NAC ]
>  [ atoms ]
>        N       NH1     -0.470  1
>        HN      H       0.310   1
>        CH3     CT3     -0.110  1
>        HH31    HA      0.090   1
>        HH32    HA      0.090   1
>        HH33    HA      0.090   1
>  [ bonds ]
>        -C      N
>        N       HN
>        N       CH3
>        CH3     HH31
>        CH3     HH32
>        CH3     HH33
>
>  [ impropers ]
>        N       -C      CH3     HN
>        -C      CH3     N       -O
>
> Mark
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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