Hi all
I would like to add to a peptide two caps in N and C term for subsequent
simulations with GMX(v4.05) with the ffG53a6 ff. For this purpose i
added manually the the missing atoms in my pdb file taken from the pdb
databank and rename the residus ACE and NH2
ATOM 1 C ACE A 145 17.175 5.988 69.357 1.00
0.00 C
ATOM 2 O ACE A 145 18.274 6.337 68.399 1.00
0.00 O
ATOM 3 C ACE A 145 17.256 4.596 68.703 1.00
0.00 C
ATOM 4 N HIS A 146 16.165 6.227 70.468 1.00
44.68 N
ATOM 5 CA HIS A 146 15.557 6.451 71.779 1.00
45.28 C
ATOM 6 C HIS A 146 14.848 5.220 72.313 1.00
42.21 C
ATOM 7 O HIS A 146 14.633 5.089 73.518 1.00
50.31 O
ATOM 8 CB HIS A 146 14.594 7.647 71.697 1.00
46.11 C
..
ATOM 62 CB ASN A 152 14.654 -14.648 73.875 1.00
42.75 C
ATOM 63 CG ASN A 152 13.199 -14.979 74.118 1.00
51.38 C
ATOM 64 OD1 ASN A 152 12.521 -15.545 73.258 1.00
63.71 O
ATOM 65 ND2 ASN A 152 12.707 -14.633 75.307 1.00
42.30 N
ATOM 66 N NH2 A 153 14.154 -16.823 71.228 1.00
0.00 N
When i use the following command: pdb2gmx_mpi -f beta-I-Ac-NH2.pdb -o
beta-I-Ac-NH2.gro -p beta-I-Ac-NH2.top -ignh
I obtain the following error
atom N not found in residue 1ACE while combining tdb and rtp
I don't understand the error since the N atom exist in my pdb. I have
take a look of the ffG53a6-n.rtp file and i found that the ACE group is
defined only with 3 atoms C, O and CA
If i use the command
pdb2gmx_mpi -f beta-I-Ac-NH2.pdb -o beta-I-Ac-NH2.gro -p
beta-I-Ac-NH2.top -ignh -ter
I have the error
Atom H not found in residue 9 while adding improper
What is wrong with my pdb file
Any advice will be appreciate
Stefane
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