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我在试验操作做的pH偏移对蛋白质的影响（就是先将pH调为2，再调回正常pH），然后我想通过动力学模拟一下这个过程中蛋白质的结构发生了什么样的变化。
然后我先跑了一个蛋白质在pH为2状态下的模拟，想利用editconf命令将最终生成的gro文件转化为pdb再进行一次pH为6的动力学模拟。为了模拟实际操作的步骤。
但是我再将转化出来的pdb文件用pdb2gmx命令导入时，会报下面这样的错误，所以我再想我这样的操作步骤是否是有误的？
“Fatal error:
Atom HE1 in residue GLN 5 was not found in rtp entry GLN with 17 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors” |
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发表于 Post on 2024-4-10 11:33:52
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发表于 Post on 2024-4-10 12:19:14
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