AMBER:处理不规则残基中遇到的问题

amber对于蛋白中的残基可以进行处理,但是Amber的标准氨基酸残基库不包含含非标准残基的原子类型和电荷. 但它们是任何分子力学模拟都必需的.所以需要单独构建残基文件,推导非标准残基的原子电荷并判定其原子类型

至于如何判断蛋白中是否存在非标准残基,除开依据经验对pdb文件进行审查之外.,就是查看导入蛋白之后报的错误了.

Loading PDB file: ./5ds3_pre.pdb

/public1/soft/amber/18-parallel-new/amber18/bin/teLeap: Warning!
Unknown residue: DSN   number: 20   type: Nonterminal
Creating new UNIT for residue: DSN sequence: 21

/public1/soft/amber/18-parallel-new/amber18/bin/teLeap: Warning!
One sided connection. Residue () missing connect0 atom.
Created a new atom named: N within residue: .R<DSN 21>
Created a new atom named: CA within residue: .R<DSN 21>
Created a new atom named: C within residue: .R<DSN 21>
Created a new atom named: O within residue: .R<DSN 21>
Created a new atom named: CB within residue: .R<DSN 21>
Created a new atom named: OG within residue: .R<DSN 21>

/public1/soft/amber/18-parallel-new/amber18/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.
  total atoms in file: 1934
  Leap added 1951 missing atoms according to residue templates:
       1951 H / lone pairs
  The file contained 6 atoms not in residue templates
Loading Mol2 file: ./olaparib.mol2
Reading MOLECULE named 09L
Checking Unit.

/public1/soft/amber/18-parallel-new/amber18/bin/teLeap: Warning!
The unperturbed charge of the unit (4.000000) is not zero.
FATAL:  Atom .R<DSN 21>.A<N 1> does not have a type.
FATAL:  Atom .R<DSN 21>.A<CA 2> does not have a type.
FATAL:  Atom .R<DSN 21>.A<C 3> does not have a type.
FATAL:  Atom .R<DSN 21>.A<O 4> does not have a type.
FATAL:  Atom .R<DSN 21>.A<CB 5> does not have a type.
FATAL:  Atom .R<DSN 21>.A<OG 6> does not have a type.

如果发生上述错误,则表示蛋白中存在非标准残基.可以参照此链接:http://ambermd.org/tutorials/basic/tutorial5/index.htm进行残基的处理.
但现在从pdb数据库中下载的残基,使用如下命令处理后

antechamber -fi ccif -i DSN.cif -bk DSN -fo ac -o dsn.ac -c bcc -at amber <
报了如下错误:

Residue CRO has a type of LINKING. Quitting/

删除下载的cif文件中的

_chem_comp.type “D-PEPTIDE LINKING” <行
又报了另外的错误

processor.acdoctor mode is on: check and diagnosis problems in the input
file.antechamber: mmcif.c:70: rmmcif: Assertion `col2 >= 0' failed.Aborted
(core dumped)*

需要定位到**$AMBERHOME/AmberTools/src/antechamber** 下的mmcif.c中的第68行那一段注释掉,也就是忽略掉蛋白分子中的LINKING部分
然后定位到当下文件夹中,重新安装antechamber

make intall

解决问题,恭喜发财!!!