On 6/27/12 12:50 PM, Shima Arasteh wrote:
OK.
PDB FILE IS AS BELOW:
HETATM 1 C FOR 0 -0.721 1.600 1.249
HETATM 2 O FOR 0 -0.839 2.806 1.453
ATOM 3 N VAL 1 -1.227 0.728 2.125
ATOM 4 CA VAL 1 -1.918 1.159 3.323
ATOM 5 C VAL 1 -1.969 2.678 3.410
ATOM 6 O VAL 1 -0.931 3.335 3.447
ATOM 7 CB VAL 1 -1.219 0.644 4.576
ATOM 8 CG1 VAL 1 0.208 1.178 4.618
ATOM 9 CG2 VAL 1 -1.976 1.118 5.812
ATOM 10 N SER 2 -3.181 3.235 3.442
ATOM 11 CA SER 2 -3.363 4.671 3.524
ATOM 12 CB SER 2 -4.138 5.196 2.320
ATOM 13 OG SER 2 -4.296 6.612 2.437
ATOM 14 C SER 2 -4.135 5.054 4.778
ATOM 15 O SER 2 -5.272 4.628 4.966
The error comes from the VAL residue (residue 2 in the sequence based on the
internal numbering used by pdb2gmx, as I suspected earlier). Note the following
line in the [impropers] section of aminoacids.rtp in the [VAL] entry:
-C -CA N -O
The improper is defined using the position of a CA atom in the preceding
residue, which in this case does not exist because it is not a normal amino acid
(though an ACE cap will also work because its atoms are named suitably). This
method of defining the improper is somewhat odd. Using a more modern force
field like Gromos96 53a6 does not give rise to this error, as all impropers are
defined using only -C or +N. Just another reason to use a non-deprecated force
field :)
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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