On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
On 5/12/12 1:32 PM, Shima Arasteh wrote:
Dear gmx users,
I want to simulate a peptide in water. The peptide has a formyl residue as the
N-terminus. I got the parameters of it and then add it to the .rtp file of
charmm36.ff as below:
[ For ]
[ atoms ]
; name type charge chargegroup
C C 0.4500 0
O O -0.5700 0
[ bonds ]
; ai aj fu b0 kb, b0 kb
1 2 1 0.12220 779866.6 0.12220 779866.6
[ pairs ]
; ai aj fu
[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 123.4390 403.48 123.4390 403.48
2 1 4 1 123.4390 403.48 123.4390 403.48
[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
But when I do what I described, I face this fatal error:
Fatal error:
No atoms found in .rtp file in residue pairs
Would you help me with this problem? Did I add the formyl in a wrong way?
Your [pairs] directive is empty, hence the error. Your [dihedrals] directive
will also produce the same error. There are no possible pairs in a unit
containing so few atoms, so you don't even need this. You may need to define
dihedrals, however, but they also depend upon the next residue.
You also have several other mistakes:
1. A formyl group has a proton on it; yours has none
2. Your net charge on the formyl group is not zero, though this may or may not
be a consequence of point #1
3. There is no connectivity information for linking to the next residue, which
will mean the formyl group will not be chemically bonded. This also affects your
dihedrals.
Another that I just caught as I hit send:
4. In your [bonds] and [angles] directives, you use atom numbers - they should
be names
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
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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