| Issue 1525: | pdb2gmx error with PGLU N-terminal residue in OPLS-AA | |
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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
Aug 13, 2012
Project Member
#1
bklarson@gmail.com
Status:
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