Krzysztof Kuczera wrote:
Hi GMXers,
I am interested in simulating blocked peptides with CHARMM (and other
force fields), using gromacs-4.5, and would appreciate some help from
more experienced GROMACS users on details.
To test things out I made a stab at creating an ACE N-terminal patch -
this exists in OPLSAA, AMBER and CHARMM, so I added this to
charmm27.ff/aminoacids.n.tdb:
[ ACE ]
[ add ]
1 2 CY N CA C
C 12.01100 0.51
1 2 OY CY N CA
O 15.99900 -0.51
1 1 CAY CY OY N
CT3 12.01100 -0.27
3 4 HY CAY CY N
HA 1.00800 0.09
[ impropers ]
CY CAY N OY
N CY CA HN
[ cmap ]
CY N CA C +N
Then built the top file with:
pdb2gmx -f -inter ala5_alpha.pdb -p ala5.top -o ala5.gro -ff charmm27
-water tip3p -nochargegrp
selecting ACE/CT2 as my terminal types
The ala5.gro geometry looks fine, but in the ala5.top file there is no
bond between atoms 2 and 7 (CY==OY in the patch), so the OY oxygen
starts to drift off in EM and MD. All other bonds are generated.
Can you tell me what is wrong here? Maybe somebody has already made a
patch that works?
Nowhere in the .tdb entry is such a bond specified, nor can it be. The correct
approach is to define .rtp entries, i.e.:
http://lists.gromacs.org/pipermail/gmx-users/2010-July/052270.html
-Justin
I attach the ala5_alpha.pdb file
Krzysztof
--
========================================
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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