[AMBER] possible bug in charmmlipid2amber.py

From: liu junjun <ljjlp03.gmail.com>
Date: Mon, 22 Apr 2019 15:14:17 +0800

Dear All,

I tried using charmmlipid2amber.py of Amber18(2.0.3) to convert lipid PDB
generated from CharmmGUI. I got the following error:

---
Error: Number of atoms in residue does not match number of atoms in residue
in replacement data file
---
I figure out that there are several TIP3P residues with id exceeding 9999.
These residues with identical id cause the above error, even though the TER
tags have been added to separate them:
---
TER
ATOM  *****  OH2 TIP3 10000     12.659  24.337 133.555  1.00  0.00      TIP3
ATOM  *****  H1  TIP3 10000     12.401  23.930 132.721  1.00  0.00      TIP3
ATOM  *****  H2  TIP3 10000     12.709  25.292 133.334  1.00  0.00      TIP3
TER
ATOM  *****  OH2 TIP3 10000      1.853  18.991 149.284  1.00  0.00      TIP3
ATOM  *****  H1  TIP3 10000      1.989  18.262 148.661  1.00  0.00      TIP3
ATOM  *****  H2  TIP3 10000      1.839  19.785 148.716  1.00  0.00      TIP3
TER
----
By checking the code of charmmlipid2amber.py, it looks like the program
basically ignores the TER tag. I did the following change, then my PDB file
can be processed correctly:
---
at line 96, change:
current_residue = previous_residue
--to-->
current_residue = ""
---
Another alternative solution to this problem could be replacing TER to some
other characters, e.g:
XXX
ATOM  *****  OH2 TIP3 10000     12.659  24.337 133.555  1.00  0.00      TIP3
ATOM  *****  H1  TIP3 10000     12.401  23.930 132.721  1.00  0.00      TIP3
ATOM  *****  H2  TIP3 10000     12.709  25.292 133.334  1.00  0.00      TIP3
XXX
Hope this helps people encountering this problem.
All the best,
Junjun
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Received on Mon Apr 22 2019 - 00:30:02 PDT