分子动力学模拟载入蛋白参数时报错

mskk

蛋白去氢：reduce -Trim 4ntr.pdb > 4ntr_removeH.pdb
建模：tleap
载入力场：source leaprc.protein.ff19SB
载入蛋白：pro = loadpdb 4ntr_removeH.pdb时，报错如下    求大神告知错误地方和解决办法


> pro = loadpdb 4ntr_removeH.pdb
Loading PDB file: ./4ntr_removeH.pdb

Warning: Unknown residue: SAR   number: 10   type: Nonterminal

Warning: Unknown residue: SAR   number: 23   type: Nonterminal

Warning: Unknown residue: SAR   number: 36   type: Nonterminal
Creating new UNIT for residue: SAR sequence: 12

Warning: One sided connection. Residue () missing connect0 atom.
Created a new atom named: N within residue: .R<SAR 12>
Created a new atom named: CA within residue: .R<SAR 12>
Created a new atom named: C within residue: .R<SAR 12>
Created a new atom named: O within residue: .R<SAR 12>
Created a new atom named: CN within residue: .R<SAR 12>

Warning: One sided connection. Residue (default_name) missing connect1 atom.
  Added missing heavy atom: .R<CVAL 14>.A<OXT 17>
Creating new UNIT for residue: SAR sequence: 25

Warning: One sided connection. Residue () missing connect0 atom.
Created a new atom named: N within residue: .R<SAR 25>
Created a new atom named: CA within residue: .R<SAR 25>
Created a new atom named: C within residue: .R<SAR 25>
Created a new atom named: O within residue: .R<SAR 25>
Created a new atom named: CN within residue: .R<SAR 25>

Warning: One sided connection. Residue (default_name) missing connect1 atom.
  Added missing heavy atom: .R<CVAL 27>.A<OXT 17>
Creating new UNIT for residue: SAR sequence: 38

Warning: One sided connection. Residue () missing connect0 atom.
Created a new atom named: N within residue: .R<SAR 38>
Created a new atom named: CA within residue: .R<SAR 38>
Created a new atom named: C within residue: .R<SAR 38>
Created a new atom named: O within residue: .R<SAR 38>
Created a new atom named: CN within residue: .R<SAR 38>

Warning: One sided connection. Residue (default_name) missing connect1 atom.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: In CONECT record for atom serial number (620)
ignoring bonded atom serial number (628) that is greater than
the maximum serial number inputted (624) from the pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Illegal CONECT record in pdb file.

Warning: Ignoring CONECT record for atom serial number (628) that is greater than
the maximum serial number inputted (624) from the pdb file.
  Added missing heavy atom: .R<CVAL 40>.A<OXT 17>
  total atoms in file: 300
  Leap added 309 missing atoms according to residue templates:
       3 Heavy
       306 H / lone pairs
  The file contained 15 atoms not in residue templates

mskk

低调的板凳 发表于 2024-6-28 10:46
肌氨酸这种N甲基化的非标准氨基酸算很不常见的了。 我找了几个之前的非标准氨基酸文件，都没有肌氨酸的。 ...

好的好的  那也非常感谢你了 这么麻烦你

平湖片帆

找不到非标准氨基酸参数文件的话，可以自己使用量化优化结构，然后生成。希望这一篇教程对你有帮助：https://ambermd.org/tutorials/basic/tutorial5/index.php

低调的板凳

mskk 发表于 2024-6-27 17:49
感谢大神   没有SAR拓扑文件   就没有其它解决方法了吗

肌氨酸这种N甲基化的非标准氨基酸算很不常见的了。 我找了几个之前的非标准氨基酸文件，都没有肌氨酸的。21年那篇charmm36力场加300多个非标准氨基酸参数的文章里都没看到SAR的数据。

student0618

沒有參數的話amber 也不會懂得模擬哦
查查有沒有literature提供適合在amberff19sb力場使用的文件 沒有的話就要自己預備了

mskk

student0618 发表于 2024-6-27 11:28
You have modified residue (SAR) that is not in the AmberFF19SB forcefield. Check if you need that mo ...

感谢大神   没有SAR拓扑文件   就没有其它解决方法了吗

student0618

You have modified residue (SAR) that is not in the AmberFF19SB forcefield. Check if you need that modification. If it's needed for your study, either search for parameters in literature or prepare their topology files. You will need to load that topology files into tleap.