Dear Justin,
Thank you very much for your quick response, which put me on the right
track.
Of course, I have some more questions and comments.
1. Putting residues in .rtp means adding ACE to the peptide sequence.
This is not the CHARMM convention, where all blocking groups are handled
through patches to existing residues. The advantage of the .rtp route is
that this makes the treatment consistent with the other implemented
force fields.
2. I believe the residues from the email need a little tweaking for
consistency with CHARMM topology/parameters.
[ ACE ] needs an extra improper and a CMAP term:
[ impropers ]
+N CH3 CA +HN
[ cmap ]
C +N +CA +C
and [ NAC ] needs a CMAP term
[ cmap ]
-N -CA -C N
3. Why won't the .n.tdb approach work?
The other reason I went with the .n.tdb file was that the amide (CT2) and
N-methylamide (CT3) C-terminals are already implemented in the .c.tdb
(CT3 is equivalent to the emailed NAC, with CMAP included). Belatedly,
I see that the authors of CT3 also had problems with missing bonds, and
added
one in explicitly - I will try that and check my .top file for energy terms.
Thanks
Krzysztof
On 9/17/10 5:14 PM, Justin A. Lemkul wrote:
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
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
