Issue 1525: pdb2gmx error with PGLU N-terminal residue in OPLS-AA
Status:  Invalid
Owner: ----
Closed:  Aug 2012
Reported by bio...@gmail.com, Aug 13, 2012
This is a copy of the Redmine #804 bug report (http://redmine.gromacs.org/issues/804):

Dear Gromacs developpers,

When I execute pdb2gmx (4.5.4) with a peptide containing the PGLU residue and OPLS-AA FF I obtain an error, by choosing None as N-terminus type (see log_error.txt file in attached archive for the complete output):

##############################

    pdb2gmx -f test_PGLU.pdb -p test_PGLU.top -o test_PGLU.gro -ff oplsaa -ter -ignh -water tip4p

...
Identified residue PGLU1 as a starting terminus.
Identified residue GLY2 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for PGLU-1
0: NH3+
1: ZWITTERION_NH3+
2: NH2
3: None
3
Start terminus PGLU-1: None
Select end terminus type for GLY-2
0: GLY-COO-
1: GLY-ZWITTERION_COO-
2: GLY-COOH
3: None
2
End terminus GLY-2: GLY-COOH

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2top.c, line: 1035

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
------------------------------------------------------- ##############################

The only solution that I found for this problem was to modify the oplsaa.ff/aminoacids.n.tdb file, by adding at the end a new entry for PGLU N-terminus, containing these 3 lines:

[ PGLU-NH ]
[ replace ]
CA opls_246 12.011 0.14

After this modification, everything works fine by choosing the new PGLU-NH N-terminus (see log_successful.txt file in attached archive for the complete output):

##############################

    pdb2gmx -f test_PGLU.pdb -p test_PGLU.top -o test_PGLU.gro -ff oplsaa -ter -ignh -water tip4p

...
Identified residue PGLU1 as a starting terminus.
Identified residue GLY2 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for PGLU-1
0: PGLU-NH
1: NH3+
2: ZWITTERION_NH3+
3: NH2
4: None
0
Start terminus PGLU-1: PGLU-NH
Select end terminus type for GLY-2
0: GLY-COO-
1: GLY-ZWITTERION_COO-
2: GLY-COOH
3: None
2
End terminus GLY-2: GLY-COOH
Checking for duplicate atoms....
Now there are 2 residues with 23 atoms
Making bonds...
Number of bonds was 23, now 23
Generating angles, dihedrals and pairs...
Before cleaning: 53 pairs
Before cleaning: 58 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 58 dihedrals, 3 impropers, 40 angles
53 pairs, 23 bonds and 0 virtual sites
Total mass 186.168 a.m.u.
Total charge 0.000 e
Writing topology

Writing coordinate file...
--------- PLEASE NOTE ------------
You have successfully generated a topology from: test_PGLU.pdb.
The Oplsaa force field and the tip4p water model are used.
--------- ETON ESAELP ------------ ##############################

Could you please implement this modification in a future version of Gromacs? Maybe it would be also useful to rename this PGLU residue into PCA, as it exists in the PDB (http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=PCA)...

Thank you in advance. Best regards,
Bogdan

Gromacs_4.5.4_oplsaa_PGLU_bug.tar.gz
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Aug 13, 2012
Project Member #1 bklarson@gmail.com
(No comment was entered for this change.)
Status: Invalid