标题: APBS计算DNA大分子静电势电荷不为整数求助 [打印本页] 作者Author: landian666 时间: 2021-8-18 13:18 标题: APBS计算DNA大分子静电势电荷不为整数求助 用APBS计算DNA大分子的静电势，因残基电荷不为零而报错退出，不管网络版还是用安装的PDB2PQR和APBS都不行，对于DNA,单个碱基电荷本来就不是整数，但整体是整数，求助怎么解决，下面是log内容，谢谢！
2021-08-18 02:43:09,342 INFO:main.py:235:print_splash_screen:PDB2PQR v3.1.0: biomolecular structure conversion software.
2021-08-18 02:43:09,342 INFO:main.py:237:print_splash_screen:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018).
2021-08-18 02:43:09,342 INFO:main.py:237:print_splash_screen:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2021-08-18 02:43:09,342 INFO:main.py:728:main_driver:Checking and transforming input arguments.
2021-08-18 02:43:09,343 INFO:main.py:732:main_driver:Loading topology files.
2021-08-18 02:43:09,409 INFO:main.py:734:main_driver:Loading molecule: aptamer-str1.pdb
2021-08-18 02:43:09,414 INFO:main.py:737:main_driver:Dropping water from structure.
2021-08-18 02:43:09,415 INFO:main.py:739:main_driver:Setting up molecule.
2021-08-18 02:43:09,420 INFO:main.py:405:setup_molecule:Created biomolecule object with 27 residues and 870 atoms.
2021-08-18 02:43:09,420 INFO:main.py:743:main_driver:Setting termini states for biomolecule chains.
2021-08-18 02:43:09,422 INFO:main.py:589:non_trivial:Loading forcefield.
2021-08-18 02:43:09,430 INFO:main.py:593:non_trivial:Loading hydrogen topology definitions.
2021-08-18 02:43:09,431 INFO:main.py:455:is_repairable:This biomolecule is clean. No repair needed.
2021-08-18 02:43:09,431 INFO:main.py:607:non_trivial:Updating disulfide bridges.
2021-08-18 02:43:09,431 INFO:main.py:610:non_trivial:Debumping biomolecule.
2021-08-18 02:43:09,434 INFO:main.py:626:non_trivial:Adding hydrogens to biomolecule.
2021-08-18 02:43:09,434 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,434 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,435 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,435 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,435 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,435 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,436 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,436 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,436 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,436 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,436 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,437 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,437 WARNING:biomolecule.py:357:add_hydrogens:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug).
2021-08-18 02:43:09,437 INFO:main.py:629:non_trivial:Debumping biomolecule (again).
2021-08-18 02:43:09,440 INFO:main.py:631:non_trivial:Optimizing hydrogen bonds
2021-08-18 02:43:09,442 INFO:main.py:643:non_trivial:Applying force field to biomolecule states.
2021-08-18 02:43:09,443 CRITICAL:main.py:768:main_driver:Residue DA5 1 charge is non-integer: 0.7143
2021-08-18 02:43:09,443 CRITICAL:main.py:769:main_driver:Giving up. 作者Author: landian666 时间: 2021-9-4 10:21 尚未解决作者Author: landian666 时间: 2021-12-27 15:01
尚未解决