Dear all,
I built a triple helix with 2 GLN and 1 SER being the first residue of the
three chains. However, while using pdb2gmx -f 1.pdb -o complex.gro -ignh -ter
-ff gromos54a7 -water SPC and choosing NH2 or NH3+ as the start terminus type
for GLN-1 and SER-1, I came across the following warnings:
WARNING: WARNING: Residue 1 named GLN (SER) of a molecule in the input file was
mapped to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the input file.
Perhaps your atom and/or residue naming needs to be fixed.
Then, I checked the .pdb and .rtp files. The difference between GLN-1/SER-1 and
GLN-n/SER-n (n>1) is that GLN-1/SER-1 contains 2 more H atoms.
Residue GLN-1 in .pdb
ATOM 1 N GLN A 1 -10.554 16.421 -0.030 1.00 0.00 N1+
ATOM 2 CA GLN A 1 -10.080 16.667 1.238 1.00 0.00 C
ATOM 3 C GLN A 1 -9.305 15.495 1.835 1.00 0.00 C
ATOM 4 O GLN A 1 -9.636 14.335 1.608 1.00 0.00 O
ATOM 5 CB GLN A 1 -11.222 17.053 2.210 1.00 0.00 C
ATOM 6 CD GLN A 1 -11.943 17.895 4.480 1.00 0.00 C
ATOM 7 NE2 GLN A 1 -11.643 18.268 5.719 1.00 0.00 N
ATOM 8 OE1 GLN A 1 -13.093 17.905 4.041 1.00 0.00 O
ATOM 9 CG GLN A 1 -10.784 17.445 3.612 1.00 0.00 C
ATOM 10 HE2 GLN A 1 -12.366 18.573 6.339 1.00 0.00 H
ATOM 11 HE2 GLN A 1 -10.694 18.243 6.032 1.00 0.00 H
ATOM 12 H GLN A 1 -11.086 17.245 -0.422 1.00 0.00 H
ATOM 13 H GLN A 1 -9.773 16.207 -0.708 1.00 0.00 H
ATOM 14 H GLN A 1 -11.212 15.593 -0.048 1.00 0.00 H
Parameters in .rtp in gromos54a7
[ GLN ]
[ atoms ]
N N -0.31000 0
H H 0.31000 0
CA CH1 0.00000 1
CB CH2 0.00000 1
CG CH2 0.00000 1
CD C 0.29000 2
OE1 O -0.45000 2
NE2 NT -0.72000 2
HE21 H 0.44000 2
HE22 H 0.44000 2
C C 0.450 3
O O -0.450 3
[ angles ]
; ai aj ak gromos type
-C N H ga_32
-C N CA ga_31
H N CA ga_18
N CA CB ga_13
N CA C ga_13
CB CA C ga_13
CA CB CG ga_15
CB CG CD ga_15
CG CD OE1 ga_30
CG CD NE2 ga_19
OE1 CD NE2 ga_33
CD NE2 HE21 ga_23
CD NE2 HE22 ga_23
HE21 NE2 HE22 ga_24
CA C O ga_30
CA C +N ga_19
O C +N ga_33
Further, I compared atoms of GLN in .pdb and .rtp, and changed 2 HE into HE21
and HE22, but got the same warnings.
The simulation can be move forward to EM and NPT smoothly. Does this kind of
warning affect the simulation results significantly?
Thanks in advance.
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