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Questions and answers => MD simulations => Topic started by: mouxuank on May 27, 2024, 04:03:40 am

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Title: Gromacs missing ' P ' atom
Post by: mouxuank on May 27, 2024, 04:03:40 am

When I used "find_pair 0.pdb | analyze" to analyze the Gromacs simulation output pdb file, I got the following tips, whether this affects the result and how I should solve the problem.

'''
handling file <0.pdb>

Time used: 00:00:00:00
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP1' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP2' atom : residue name ' DG', chain  , number [   1 ]
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP1' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP2' atom : residue name ' DG', chain  , number [   1 ]
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]

Time used: 00:00:00:01
'''

Title: Re: Gromacs missing ' P ' atom
Post by: xiangjun on May 27, 2024, 06:41:08 pm

No, it is for information only: i.e., the first nucleotide (DG1) does not have the phosphate group.

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