Hello Amber users,
I am using amber-10. I wish to protonate a complex for which I gave
following commands-
1. ~/src/Xtruct/trunk/amber_10_install/bin/protonate -k -d
~/src/Xtruct/trunk/amber_10_install/dat/PROTON_INFO -i
complex-from-chimera.pdb -o complex.pdb -l protonate-com.out
The file "protonate-com.out" contains these lines -
Here are the mystery protons from input file:
HD1 HIE 973 -6.92 8.32 35.72
HG CYS1168 -43.37 -0.32 57.45
HD1 HIE1177 -42.26 7.20 61.09
HAV DXQ2000 -41.51 14.55 48.53
HBE DXQ2000 -42.88 15.99 47.73
HAL2 DXQ2000 -41.59 17.54 49.27
HAL3 DXQ2000 -40.79 18.17 47.82
HAQ2 DXQ2000 -42.81 19.52 48.28
HAQ3 DXQ2000 -43.81 18.03 48.34
HBH DXQ2000 -42.45 19.30 46.02
HAP2 DXQ2000 -42.87 17.66 44.52
HAP3 DXQ2000 -43.90 16.75 45.66
HAK2 DXQ2000 -41.80 15.56 45.50
HAK3 DXQ2000 -40.85 17.03 45.75
HAG DXQ2000 -41.16 13.11 49.10
HAJ2 DXQ2000 -35.87 10.28 50.26
HAJ3 DXQ2000 -36.46 9.56 48.79
HAH2 DXQ2000 -35.57 7.98 50.67
HAH3 DXQ2000 -37.10 8.15 51.33
HBF DXQ2000 -37.21 7.41 48.09
HAF DXQ2000 -36.34 12.11 49.03
HAS2 DXQ2000 -38.15 17.80 46.29
HAS3 DXQ2000 -36.54 18.21 45.70
HAR2 DXQ2000 -37.41 19.78 47.50
HAR3 DXQ2000 -37.39 18.40 48.64
HBG DXQ2000 -34.97 19.06 47.10
HAN2 DXQ2000 -34.14 18.50 49.52
HAN3 DXQ2000 -35.72 17.66 49.56
HAI2 DXQ2000 -34.11 16.05 48.86
HAI3 DXQ2000 -33.34 17.16 47.74
HAO2 DXQ2000 -34.74 16.64 46.04
HAO3 DXQ2000 -34.99 15.19 46.97
HAB1 DXQ2000 -39.47 6.59 48.57
HAB2 DXQ2000 -38.66 5.11 49.19
HAB3 DXQ2000 -38.45 5.62 47.55
HAC1 DXQ2000 -35.27 6.34 48.97
HAC2 DXQ2000 -36.20 5.48 47.71
HAC3 DXQ2000 -36.38 4.98 49.42
HAD1 DXQ2000 -34.30 20.60 48.84
HAD2 DXQ2000 -35.77 21.15 47.97
HAD3 DXQ2000 -35.92 20.39 49.59
HAE1 DXQ2000 -44.64 20.07 46.75
HAE2 DXQ2000 -44.60 19.41 45.08
HAE3 DXQ2000 -45.26 18.41 46.42
HAA1 DXQ2000 -42.51 10.24 50.49
HAA2 DXQ2000 -42.13 11.98 50.63
HAA3 DXQ2000 -42.22 11.21 49.02
HAA3 DXQ2000 -42.22 11.21 49.02
~
Also, final complex does not have hydrogen atoms on ligand (DXQ). Could you
point out what the problem is. I generated parameters for DXQ using
antechamber. do I need to use them somewhere?
Further I wish to use
2. ambpdb -pqr -p complex.prmtop < complex.inpcrd > complex.pqr
3. pol_h < complex.pqr > complex-1.pdb
Will I need to specify frcmod file for DXQ in pol_h command ?
Thank you
Regards,
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Received on Mon Aug 16 2010 - 01:00:03 PDT
