求助：Antechamber计算多肽的电荷问题

ezez

一个八肽和受体蛋白用vina对接后，想用amber跑md，先用antechamber计算多肽电荷，按照官网教程（不过官网的小分子是化合物，我这个是多肽），命令如下：
antechamber -i UNK.pdb -fi pdb -o UNK.mol2 -fo mol2 -c bcc -s 2

返回报错如下：
Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
      for those not bonded   
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: N1) and (ID: 97, Name: N15).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: N2) and (ID: 98, Name: N16).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: N3) and (ID: 99, Name: N17).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: N4) and (ID: 100, Name: N18).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: N5) and (ID: 101, Name: N19).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: N6) and (ID: 102, Name: N20).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: N7) and (ID: 103, Name: N21).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: N8) and (ID: 104, Name: N22).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: N9) and (ID: 105, Name: N23).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: N10) and (ID: 106, Name: N24).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: N11) and (ID: 107, Name: N25).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: N12) and (ID: 108, Name: N26).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: N13) and (ID: 109, Name: N27).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: N14) and (ID: 110, Name: N28).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: C1) and (ID: 111, Name: C55).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: C2) and (ID: 112, Name: C56).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: C3) and (ID: 113, Name: C57).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: C4) and (ID: 114, Name: C58).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: C5) and (ID: 115, Name: C59).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: C6) and (ID: 116, Name: C60).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: C7) and (ID: 117, Name: C61).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: C8) and (ID: 118, Name: C62).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: C9) and (ID: 119, Name: C63).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: C10) and (ID: 120, Name: C64).
Warning: Close ( 0.00) nonbonded atoms (ID: 25, Name: C11) and (ID: 121, Name: C65).
Warning: Close ( 0.00) nonbonded atoms (ID: 26, Name: C12) and (ID: 122, Name: C66).
Warning: Close ( 0.00) nonbonded atoms (ID: 27, Name: C13) and (ID: 123, Name: C67).
Warning: Close ( 0.00) nonbonded atoms (ID: 28, Name: C14) and (ID: 124, Name: C68).
Warning: Close ( 0.00) nonbonded atoms (ID: 29, Name: C15) and (ID: 125, Name: C69).
Warning: Close ( 0.00) nonbonded atoms (ID: 30, Name: C16) and (ID: 126, Name: C70).
Warning: Close ( 0.00) nonbonded atoms (ID: 31, Name: C17) and (ID: 127, Name: C71).
Warning: Close ( 0.00) nonbonded atoms (ID: 32, Name: C18) and (ID: 128, Name: C72).
Warning: Close ( 0.00) nonbonded atoms (ID: 33, Name: C19) and (ID: 129, Name: C73).
Warning: Close ( 0.00) nonbonded atoms (ID: 34, Name: C20) and (ID: 130, Name: C74).
Warning: Close ( 0.00) nonbonded atoms (ID: 35, Name: C21) and (ID: 131, Name: C75).
Warning: Close ( 0.00) nonbonded atoms (ID: 36, Name: C22) and (ID: 132, Name: C76).
Warning: Close ( 0.00) nonbonded atoms (ID: 37, Name: C23) and (ID: 133, Name: C77).
Warning: Close ( 0.00) nonbonded atoms (ID: 38, Name: C24) and (ID: 134, Name: C78).
Warning: Close ( 0.00) nonbonded atoms (ID: 39, Name: C25) and (ID: 135, Name: C79).
Warning: Close ( 0.00) nonbonded atoms (ID: 40, Name: C26) and (ID: 136, Name: C80).
Warning: Close ( 0.00) nonbonded atoms (ID: 41, Name: C27) and (ID: 137, Name: C81).
Warning: Close ( 0.00) nonbonded atoms (ID: 42, Name: C28) and (ID: 138, Name: C82).
Warning: Close ( 0.00) nonbonded atoms (ID: 43, Name: C29) and (ID: 139, Name: C83).
Warning: Close ( 0.00) nonbonded atoms (ID: 44, Name: C30) and (ID: 140, Name: C84).
Warning: Close ( 0.00) nonbonded atoms (ID: 45, Name: C31) and (ID: 141, Name: C85).
Warning: Close ( 0.00) nonbonded atoms (ID: 46, Name: C32) and (ID: 142, Name: C86).
Warning: Close ( 0.00) nonbonded atoms (ID: 47, Name: C33) and (ID: 143, Name: C87).
Warning: Close ( 0.00) nonbonded atoms (ID: 48, Name: C34) and (ID: 144, Name: C88).
Warning: Close ( 0.00) nonbonded atoms (ID: 49, Name: C35) and (ID: 145, Name: C89).
Warning: Close ( 0.00) nonbonded atoms (ID: 50, Name: C36) and (ID: 146, Name: C90).
Warning: Close ( 0.00) nonbonded atoms (ID: 51, Name: C37) and (ID: 147, Name: C91).
Warning: Close ( 0.00) nonbonded atoms (ID: 52, Name: C38) and (ID: 148, Name: C92).
Warning: Close ( 0.00) nonbonded atoms (ID: 53, Name: C39) and (ID: 149, Name: C93).
Warning: Close ( 0.00) nonbonded atoms (ID: 54, Name: C40) and (ID: 150, Name: C94).
Warning: Close ( 0.00) nonbonded atoms (ID: 55, Name: C41) and (ID: 151, Name: C95).
Warning: Close ( 0.00) nonbonded atoms (ID: 56, Name: C42) and (ID: 152, Name: C96).
Warning: Close ( 0.00) nonbonded atoms (ID: 57, Name: C43) and (ID: 153, Name: C97).
Warning: Close ( 0.00) nonbonded atoms (ID: 58, Name: C44) and (ID: 154, Name: C98).
Warning: Close ( 0.00) nonbonded atoms (ID: 59, Name: C45) and (ID: 155, Name: C99).
Warning: Close ( 0.00) nonbonded atoms (ID: 60, Name: C46) and (ID: 156, Name: C100).
Warning: Close ( 0.00) nonbonded atoms (ID: 61, Name: C47) and (ID: 157, Name: C101).
Warning: Close ( 0.00) nonbonded atoms (ID: 62, Name: C48) and (ID: 158, Name: C102).
Warning: Close ( 0.00) nonbonded atoms (ID: 63, Name: C49) and (ID: 159, Name: C103).
Warning: Close ( 0.00) nonbonded atoms (ID: 64, Name: C50) and (ID: 160, Name: C104).
Warning: Close ( 0.00) nonbonded atoms (ID: 65, Name: C51) and (ID: 161, Name: C105).
Warning: Close ( 0.00) nonbonded atoms (ID: 66, Name: C52) and (ID: 162, Name: C106).
Warning: Close ( 0.00) nonbonded atoms (ID: 67, Name: C53) and (ID: 163, Name: C107).
Warning: Close ( 0.00) nonbonded atoms (ID: 68, Name: C54) and (ID: 164, Name: C108).
Warning: Close ( 0.00) nonbonded atoms (ID: 69, Name: O1) and (ID: 165, Name: O11).
Warning: Close ( 0.00) nonbonded atoms (ID: 70, Name: O2) and (ID: 166, Name: O12).
Warning: Close ( 0.00) nonbonded atoms (ID: 71, Name: O3) and (ID: 167, Name: O13).
Warning: Close ( 0.00) nonbonded atoms (ID: 72, Name: O4) and (ID: 168, Name: O14).
Warning: Close ( 0.00) nonbonded atoms (ID: 73, Name: O5) and (ID: 169, Name: O15).
Warning: Close ( 0.00) nonbonded atoms (ID: 74, Name: O6) and (ID: 170, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 75, Name: O7) and (ID: 171, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 76, Name: O8) and (ID: 172, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 77, Name: O9) and (ID: 173, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 78, Name: O10) and (ID: 174, Name: O20).
Warning: Close ( 0.00) nonbonded atoms (ID: 79, Name: H1) and (ID: 175, Name: H19).
Warning: Close ( 0.00) nonbonded atoms (ID: 80, Name: H2) and (ID: 176, Name: H20).
Warning: Close ( 0.00) nonbonded atoms (ID: 81, Name: H3) and (ID: 177, Name: H21).
Warning: Close ( 0.00) nonbonded atoms (ID: 82, Name: H4) and (ID: 178, Name: H22).
Warning: Close ( 0.00) nonbonded atoms (ID: 83, Name: H5) and (ID: 179, Name: H23).
Warning: Close ( 0.00) nonbonded atoms (ID: 84, Name: H6) and (ID: 180, Name: H24).
Warning: Close ( 0.00) nonbonded atoms (ID: 85, Name: H7) and (ID: 181, Name: H25).
Warning: Close ( 0.00) nonbonded atoms (ID: 86, Name: H8) and (ID: 182, Name: H26).
Warning: Close ( 0.00) nonbonded atoms (ID: 87, Name: H9) and (ID: 183, Name: H27).
Warning: Close ( 0.00) nonbonded atoms (ID: 88, Name: H10) and (ID: 184, Name: H28).
Warning: Close ( 0.00) nonbonded atoms (ID: 89, Name: H11) and (ID: 185, Name: H29).
Warning: Close ( 0.00) nonbonded atoms (ID: 90, Name: H12) and (ID: 186, Name: H30).
Warning: Close ( 0.00) nonbonded atoms (ID: 91, Name: H13) and (ID: 187, Name: H31).
Warning: Close ( 0.00) nonbonded atoms (ID: 92, Name: H14) and (ID: 188, Name: H32).
Warning: Close ( 0.00) nonbonded atoms (ID: 93, Name: H15) and (ID: 189, Name: H33).
Warning: Close ( 0.00) nonbonded atoms (ID: 94, Name: H16) and (ID: 190, Name: H34).
Warning: Close ( 0.00) nonbonded atoms (ID: 95, Name: H17) and (ID: 191, Name: H35).
Warning: Close ( 0.00) nonbonded atoms (ID: 96, Name: H18) and (ID: 192, Name: H36).
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /opt/amber/amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Info: The number of rings (73012) exceeded the default (1000).
Warning: For atom (ID: 1, Name: N1) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 2, Name: N2) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 3, Name: N3) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 4, Name: N4) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 5, Name: N5) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 6, Name: N6) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 7, Name: N7) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 8, Name: N8) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 9, Name: N9) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 11, Name: N11) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 12, Name: N12) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 13, Name: N13) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 14, Name: N14) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 97, Name: N15) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 98, Name: N16) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 99, Name: N17) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 100, Name: N18) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 101, Name: N19) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 102, Name: N20) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 103, Name: N21) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 104, Name: N22) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 105, Name: N23) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 107, Name: N25) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 108, Name: N26) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 109, Name: N27) the best APS is not zero.
         Bonds involving this atom are frozen.
Warning: For atom (ID: 110, Name: N28) the best APS is not zero.
         Bonds involving this atom are frozen.
The frozen atom type can only be 1, 2, 3, 7 (aromatic single),
or 8 (aromatic double).
/opt/amber/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/home/sun/opt/amber/amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac".





补充说明：
同样的方法，我用来计算小分子化合物就可以，但是多肽就不行～

官网上没有搜到怎样用antechamber计算多肽的电荷，官网上只是说了让从pdb数据库里下载cif格式的蛋白文件。。。

麻烦大家了～
多谢～

sobereva

对于这类问题，用Multiwfn算RESP电荷好得多，而且对任何体系都能用，而且超级灵活，操作极其简单，看
RESP拟合静电势电荷的原理以及在Multiwfn中的计算
http://sobereva.com/441

PS：通常对于多肽类体系，应当直接用AMBER力场直接定义的氨基酸残基的原子电荷拼接来得到，而不是自己去计算（除非有非标准残基）