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 <[email protected]
<mailto:[email protected]>> wrote:
----- Original Message -----
From: Sai Pooja <[email protected] <mailto:[email protected]>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: [email protected] <mailto:[email protected]>, Discussion list for
GROMACS users <[email protected] <mailto:[email protected]>>
> 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.
--
========================================
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
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