Reply To: some application troubles when using resfile flag

[Anonymous]

Thanks for your resourceful ideas.

my backrub command was:

/home/zcc/ro/rosetta_source/bin/backrub.linuxgccrelease -database /home/zcc/ro/rosetta_database -s xxx.pdb -in:file:fullatom -ignore_unrecognized_res -pivot_residues xxx -nstruct 1 -backrub:trajectory -backrub:trajectory_stride 100 -backrub:ntrials 1000 -resfile resfile.resfile

my resfile was:

start
xx x EMPTY NC cysmtsl

my params file was:

NAME cysmtsl
IO_STRING cys X
TYPE POLYMER
AA UNK
ATOM N Nbb X -0.46
ATOM CA CAbb X -0.02
ATOM C CObb C 0.69
ATOM O OCbb O -0.48
ATOM CB CH1 X -0.02
ATOM SG S S -0.09
ATOM SD S S -0.09
ATOM CE CH2 CT2 -0.11
ATOM CZ CH1 X -0.02
ATOM CT1 CH1 X -0.02
ATOM CT2 CH2 CT2 -0.11
ATOM NI1 Nhis N -0.46
ATOM CI2 CH2 CT2 -0.11
ATOM CK CH1 X -0.02
ATOM OL OOC X -0.69
ATOM 1HE Hapo HA 0.16
ATOM 2HE Hapo HA 0.16
ATOM 1HT1 Hapo HA 0.16
ATOM 1HT2 Hapo HA 0.16
ATOM 2HT2 Hapo HA 0.16
ATOM 1HI2 Hapo HA 0.16
ATOM 2HI2 Hapo HA 0.16
ATOM 1HK Hapo HA 0.16
BOND N CA
BOND CA C
BOND CA CB
BOND C O
BOND CB SG
BOND CE SD
BOND CE CZ
BOND CE 1HE
BOND CE 2HE
BOND NI1 CI2
BOND NI1 CK
BOND NI1 CT2
BOND SG SD
BOND CT1 CI2
BOND CT1 CZ
BOND CT1 1HT1
BOND OL CK
BOND CI2 1HI2
BOND CI2 2HI2
BOND CK 1HK
BOND CT2 CZ
BOND CT2 1HT2
BOND CT2 2HT2
LOWER_CONNECT N
UPPER_CONNECT C
CHI 1 N CA C O
CHI 2 N CA CB SG
CHI 3 CA CB SG SD
CHI 4 SG SD CE CZ
CHI 5 SD CE CZ CT1
CHI 6 CI2 NI1 CK OL
CHI 7 CB SG SD CE
NBR_ATOM CB
NBR_RADIUS 12.925454
FIRST_SIDECHAIN_ATOM CB
PROPERTIES
ICOOR_INTERNAL N 0.000000 0.000000 0.000000 N CA C
ICOOR_INTERNAL CA 0.000000 180.000000 1.459903 N CA C
ICOOR_INTERNAL C 0.000000 69.006998 1.510333 CA N C
ICOOR_INTERNAL LOWER -139.014150 70.508075 1.469804 N CA C
ICOOR_INTERNAL O -45.001477 57.373553 1.189745 C CA N
ICOOR_INTERNAL UPPER 134.979634 61.316313 1.470295 C CA N
ICOOR_INTERNAL CB -124.073480 71.485237 1.540777 CA N C
ICOOR_INTERNAL SG -179.600976 69.301095 1.820495 CB CA N
ICOOR_INTERNAL SD 144.270431 70.529387 2.050335 SG CB CA
ICOOR_INTERNAL CE -3.866097 70.477679 1.820179 SD SG CB
ICOOR_INTERNAL CZ 66.627736 70.545670 1.540568 CE SD SG
ICOOR_INTERNAL CT1 38.139473 70.356167 1.534727 CZ CE SD
ICOOR_INTERNAL CI2 92.821331 76.080757 1.529982 CT1 CZ CE
ICOOR_INTERNAL NI1 38.571347 79.793405 1.477770 CI2 CT1 CZ
ICOOR_INTERNAL CK -159.657601 70.552353 1.469053 NI1 CI2 CT1
ICOOR_INTERNAL OL -58.131202 59.560957 1.208191 CK NI1 CI2
ICOOR_INTERNAL 1HK 179.911060 60.877779 1.113399 CK NI1 OL
ICOOR_INTERNAL CT2 120.200527 70.239065 1.477421 NI1 CI2 CK
ICOOR_INTERNAL 1HT2 -93.767901 70.051674 1.117109 CT2 NI1 CI2
ICOOR_INTERNAL 2HT2 -120.446653 66.389617 1.116490 CT2 NI1 1HT2
ICOOR_INTERNAL 1HI2 123.736571 67.068388 1.116479 CI2 CT1 NI1
ICOOR_INTERNAL 2HI2 121.385881 70.128788 1.117124 CI2 CT1 1HI2
ICOOR_INTERNAL 1HT1 -179.980157 51.978019 1.090371 CT1 CZ CI2
ICOOR_INTERNAL 1HE 120.028447 70.490228 1.089499 CE SD CZ
ICOOR_INTERNAL 2HE 120.042929 70.520860 1.090014 CE SD 1HE

I tried both adduct and original cys, but still did not work. What a pity…

And you said `If you name it like the adduct…` does it mean just to add a line in resfile, like what I`ve done?

Thanks very much.