[gmx-users] Add a amide and acetylated caps to a peptide with pdb2gmx

[Stephane Abel]

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