Hello,
I have a non standard residue (GFP chromophore) that I should build with
antechamber. When I try to build it using amber parameters, I just obtain some
junk output and the prepin file cannot be created.
If I try gaff parameters, I get the prepin file but head and tail atoms are not
the ones I want (I get an O atom instead of N and some side chain C atom
instead of the backbone C atom). So, I cannot build my protein using this
residue and other standard resiues.
Can somebody help me with this problem?
Thanks alot,
MuratC
Below is my input file:
ATOM 1 O3 CRO 1 -1.757 -4.399 1.616 0.00000
ATOM 2 C3 CRO 1 -0.625 -3.957 1.433 0.00000
ATOM 3 CA3 CRO 1 -0.407 -2.445 1.369 0.00000
ATOM 4 H35 CRO 1 -1.026 -2.035 0.571 0.00000
ATOM 5 H36 CRO 1 -0.721 -2.007 2.317 0.00000
ATOM 6 N3 CRO 1 0.975 -2.061 1.123 0.00000
ATOM 7 C2 CRO 1 1.665 -1.261 1.934 0.00000
ATOM 8 O2 CRO 1 1.243 -0.768 2.977 0.00000
ATOM 9 C1 CRO 1 1.562 -2.117 -0.068 0.00000
ATOM 10 CA1 CRO 1 0.744 -2.477 -1.295 0.00000
ATOM 11 N1 CRO 1 -0.161 -1.397 -1.639 0.00000
ATOM 12 H23 CRO 1 0.213 -0.471 -1.788 0.00000
ATOM 13 CB1 CRO 1 1.652 -2.770 -2.486 0.00000
ATOM 14 CG1 CRO 1 0.805 -3.237 -3.667 0.00000
ATOM 15 H26 CRO 1 0.275 -4.151 -3.397 0.00000
ATOM 16 H27 CRO 1 1.450 -3.428 -4.525 0.00000
ATOM 17 H28 CRO 1 0.082 -2.463 -3.925 0.00000
ATOM 18 OG1 CRO 1 2.577 -3.775 -2.141 0.00000
ATOM 19 H29 CRO 1 3.180 -3.898 -2.877 0.00000
ATOM 20 H25 CRO 1 2.190 -1.863 -2.761 0.00000
ATOM 21 H24 CRO 1 0.157 -3.369 -1.074 0.00000
ATOM 22 N2 CRO 1 2.582 -1.263 -0.179 0.00000
ATOM 23 CA2 CRO 1 2.809 -0.650 1.123 0.00000
ATOM 24 CB2 CRO 1 4.178 -1.059 1.659 0.00000
ATOM 25 H40 CRO 1 4.232 -0.825 2.722 0.00000
ATOM 26 CG2 CRO 1 5.326 -0.382 0.946 0.00000
ATOM 27 CD1 CRO 1 5.346 -0.326 -0.453 0.00000
ATOM 28 H43 CRO 1 4.547 -0.775 -1.024 0.00000
ATOM 29 CE1 CRO 1 6.400 0.317 -1.116 0.00000
ATOM 30 H47 CRO 1 6.414 0.362 -2.195 0.00000
ATOM 31 CZ CRO 1 7.439 0.909 -0.373 0.00000
ATOM 32 OH CRO 1 8.465 1.540 -1.014 0.00000
ATOM 33 H51 CRO 1 9.115 1.908 -0.411 0.00000
ATOM 34 CE2 CRO 1 7.416 0.849 1.034 0.00000
ATOM 35 H48 CRO 1 8.210 1.303 1.608 0.00000
ATOM 36 CD2 CRO 1 6.359 0.205 1.688 0.00000
ATOM 37 H44 CRO 1 6.337 0.164 2.768 0.00000
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Received on Sun Oct 10 2004 - 03:53:00 PDT
