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Bug #3222

editconf change the name of carbon atoms

Added by zhiyi wu 10 months ago. Updated 9 months ago.

Status:
Rejected
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Say if I had a gro file which has a atom, which is named as C116.
If I use editconf to change it to pdb, the name C116 will get changed to 6C11, which is probably a problem.
Sample gro file is attached.
gmx editconf -f AR_PC_AR.gro -o temp.pdb

AR_PC_AR.gro (6.14 KB) AR_PC_AR.gro zhiyi wu, 11/29/2019 05:42 PM

History

#1 Updated by Erik Lindahl 9 months ago

  • Status changed from New to Rejected

The reason for this is that the PDB format is more restrictive than the GRO one.

PDB has hard specifications about what column must contain the element name ("C"), and then there are two more columns available for extending the name - and in principle that's it.

Since this isn't enough, the PDB format also allows chemically identical atom suffices (think hydrogens 1 to 3 connected to a carbon names CX1, then they would be named HX11 through HX13 in the GROM file). In the PDB standard this is instead handled by putting the 1-3 suffices before the element column, so it would be 1HX1 through 3HX1. If you read this back into a GRO file, it will be corrected back.

However, there is nothing we can do to magically make more room in the PDB file while we still fulfil the standard.

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