[gmx-users] Capping residues

[Justin A. Lemkul]

Sai Pooja wrote:
> 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?

What are you choosing as your termini when running pdb2gmx?  It should be 
"none," since by capping, you are not choosing a protonation state for the N- 
and C-termini.

-Justin

> 
> Pooja
> 
> 
> On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
> 
> 
> 
>     ----- Original Message -----
>     From: Sai Pooja <saipooja at gmail.com <mailto:saipooja at gmail.com>>
>     Date: Friday, July 2, 2010 7:28
>     Subject: Re: [gmx-users] Capping residues
>     To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
>     GROMACS users <gmx-users at gromacs.org <mailto: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
>     --
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================