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Bug #373

Default ATP topology from ffG53a6 uses 5 letter atom names while in pdb files maximum atom name is 4 letter

Added by Alexey Shvetsov almost 10 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Created an attachment (id=404)
ffG53a6.hdb.diff

Default ATP topology from ffG53a6 uses 5 letter atom names while in pdb files maximum atom name is 4 letter. So pdb2gmx cannot use ATP definition in ffG53a6.rtp to generate ATP topology from pdb file.

Also there missing hydrogen definitions in ffG53a6.hdb for ATP DTHY and DADE

ffG53a6.hdb.diff (402 Bytes) ffG53a6.hdb.diff ffG53a6.hdb.diff Alexey Shvetsov, 12/02/2009 02:37 PM
ffG53a6.rtp.diff (4.48 KB) ffG53a6.rtp.diff ffG53a6.rtp.diff Alexey Shvetsov, 12/02/2009 02:38 PM

History

#1 Updated by Alexey Shvetsov almost 10 years ago

Created an attachment (id=405)
ffG53a6.rtp.diff

#2 Updated by David van der Spoel over 9 years ago

Fixed force field files for ATP in order to clear bug. However, due to inconsistencies in PDB atom naming this might not help very much. Also there is no ADP entry.

#3 Updated by Alexey Shvetsov over 9 years ago

(In reply to comment #2)

Fixed force field files for ATP in order to clear bug. However, due to
inconsistencies in PDB atom naming this might not help very much. Also there is
no ADP entry.

I can upload one =)

Also available in: Atom PDF