Serena Leone wrote:
Dear all,
I was trying to model a peptide that I built from scratch with Chimera
to use in some simulation with Gromacs 4 (encad vacuum ff). After
moduifying the atom names in the pdb accordingly to rtp for
ffencadv.rtp, I keep obtaining this error from pdb2gmx:
Program pdb2gmx, VERSION 4.0
Source code file: pgutil.c, line: 87
Fatal error:
Atom H not found in residue 3 while adding improper
Residue 3 in my case is a Pro, and, not being terminal, it is not
supposed to have an amide H. Now, I know that is usually not recommended
to play with the ff rtp files, but it seems to me an error in the rtp,
that maybe needs to be corrected:
rtp entry:
[ PRO ]
[ atoms ]
N N 0.000 0
CA C1 -0.119 1
HA H 0.119 1
CB CP -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG CP -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD CP -0.238 4
HD1 H 0.119 4
HD2 H 0.119 4
C Aprime 0.380 5
O O -0.380 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ dihedrals ]
-CA -C N CD
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG N CD HD1 improper_X_X_C_X
CG N CD HD2 improper_X_X_C_X
-C CD N CA improper_X_X_N_X
CA +N C O improper_X_X_A_X
Now, my guess would be, to describethe same improper, that it should read:
-C CA N CD improper_X_X_N_X
instead of
-C CA N H improper_X_X_N_X
am I right, or am I overlooking something?
I don't know anything about this force field, but the line under
discussion was not present in 3.3.x versions of GROMACS. Improper
dihedrals are used to help enforce planarity of four atoms. As such,
only two are required to keep -CA, -C, -O, N, H, CA moiety coplanar
given the existence of a -CA, -C, N, C normal dihedral. All the other
peptide linkages have only the two impropers as indicated in the last
two lines of [impropers] for PRO above. Thus, I think this proline
residue topology got broken in the source distribution between the 3.3.1
version I'm looking at, and 4.0.
Mark
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