12 December 2015 3 7K Report

I want to optimize reference ligand of my target protein (1M48) before running Molecular Dynamic Simultion. I have prepared reference ligand mol2 file through moe and then convert it into com format without changing coordinates but after resp charge calculation my ligand atom typing is disturbed specially guanidine, amide and carbon carbon triple bond of my ligand. Would anyone please give me some suggestions regrading this. My input file is like this,

%chk=frg.chk

%mem=2GB

%nproc=2

#P HF/6-31G* SCF=Tight nosymm Geom=Connectivity Pop=MK IOp(6/33=2,6/41=10,6/42=17)

frg_resp

+1 1

N 2.56400000 20.96500000 0.10200000

H 1.74330000 21.53320000 0.25620000

H 3.35510000 21.04090000 0.72530000

C 2.60300000 20.11500000 -0.92400000

N 3.66400000 19.30900000 -1.00600000

H 4.39240000 19.36040000 -0.30820000

H 3.73840000 18.64780000 -1.76580000

N 1.46400000 20.01000000 -1.81600000

C 1.54400000 18.89100000 -2.79600000

H 0.60470000 18.34020000 -2.74730000

H 2.36300000 18.24030000 -2.48960000

C 0.77700000 21.25900000 -2.26300000

H 1.25520000 22.09770000 -1.75700000

H -0.26500000 21.19230000 -1.95030000

C 0.79200000 21.55500000 -3.76800000

H 1.69790000 22.11940000 -3.98900000

H -0.08140000 22.16530000 -3.99770000

C 0.76500000 20.33400000 -4.68500000

H 0.99510000 20.65170000 -5.70200000

H -0.23240000 19.89510000 -4.65840000

C 1.78000000 19.27900000 -4.25600000

H 2.78160000 19.69910000 -4.34800000

C 1.70100000 18.04000000 -5.17200000

H 0.73200000 17.55950000 -5.03720000

H 2.49320000 17.34360000 -4.89710000

C 1.86400000 18.42400000 -6.63000000

O 2.92900000 18.87900000 -7.00900000

N 0.81300000 18.25200000 -7.45500000

H -0.07420000 17.96830000 -7.06450000

C 0.91700000 18.46400000 -8.90300000

H 1.93290000 18.18860000 -9.18610000

C 0.79700000 19.91000000 -9.32700000

O 1.47200000 20.37900000 -10.23500000

O -0.10900000 20.80100000 -8.61900000

C -0.44000000 22.08800000 -9.14000000

H -1.12840000 22.58930000 -8.45960000

H -0.91190000 21.97450000 -10.11600000

H 0.46750000 22.68300000 -9.24230000

C -0.04500000 17.55600000 -9.64200000

H 0.14160000 17.70850000 -10.70500000

H -1.04830000 17.90360000 -9.39570000

C -0.04300000 16.09200000 -9.42200000

C -1.04300000 15.46700000 -8.68000000

H -1.82690000 16.06130000 -8.23420000

C -1.04400000 14.09100000 -8.50700000

H -1.82710000 13.59910000 -7.94920000

C 0.97200000 15.33600000 -9.99400000

H 1.74430000 15.81910000 -10.57420000

C 0.99300000 13.97100000 -9.82100000

H 1.77860000 13.37500000 -10.26160000

C -0.01000000 13.37100000 -9.07200000

C 0.04500000 11.93000000 -8.93200000

C 0.11400000 10.63800000 -8.86200000

C 0.16000000 9.19500000 -8.82400000

C -0.69900000 8.50900000 -9.66900000

H -1.36430000 9.04780000 -10.32740000

C -0.69300000 7.12800000 -9.65800000

H -1.34200000 6.56660000 -10.31380000

C 1.01600000 8.56700000 -7.95600000

H 1.66230000 9.13280000 -7.30130000

C 1.02300000 7.18900000 -7.94800000

H 1.69550000 6.65850000 -7.29030000

C 0.16800000 6.47900000 -8.78300000

H 0.17350000 5.39950000 -8.75050000

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