[gmx-users] topology for small peptide using amber03

kolnkempff kolnkempff at gmail.com
Thu Nov 28 04:21:19 CET 2013


/I am trying to use pdb2gmx to get a topology for a very simple peptide that
has just three components:  an ACE residue followed by phenylananine
followed by NME
I've read through the Duan article and it seems that amber03 should be ideal
for this.  The pdb file I'm using came from a quantum simulation using
gamess.  I went in by hand to label each atom as belonging to ACE, PHE, or
NME.

Try #1  All atoms listed as "HETATM"/

Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/dna.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/rna.r2b
Reading apn1.pdb...
WARNING: all CONECT records are ignored
Read 'UNNAMED', 32 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 32 atoms

  chain  #res #atoms
  1 ' '     3     32  

All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber03)
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.c.tdb
Processing chain 1 (32 atoms, 3 residues)
Identified residue PHE1 as a starting terminus.
Identified residue NME1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.4
Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/pdb2gmx.c, line:
727

Fatal error:
Atom H in residue ACE 1 was not found in rtp entry ACE with 6 atoms
while sorting atoms.

/I looked at aminoacids.rtp which lists [ACE] as having 6 atoms.  I went
ahead and checked [PHE] and [NME] and I have the same number and type of
atoms as they do.

Try #2.  After looking at a pdb file for a small neuropeptide I decided to
try labeling everything as "ATOM" rather than 'HETATM"
[first part is same as before]/

Warning: Starting residue E1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.4
Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/resall.c, line:
642

Fatal error:
Residue 'E' not found in residue topology database

/Try #3.  I labeled the phenylalanine atoms as "ATOM" and the terminal ACE
and NME atoms as "HETATM"/
Warning: Starting residue E1 in chain not identified as Protein/RNA/DNA.
Identified residue ACE1 as a starting terminus.
Identified residue NME1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.4
Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/resall.c, line:
642

Fatal error:
Residue 'E' not found in residue topology database

/I have no idea where "Residue 'E'" came from.
Since the third try seems to be closest to "working", that's the one I am
including below.

Thanks in advance for whatever help you can offer.

Koln/

pdb file:COMPND    UNNAMED
AUTHOR    GENERATED BY OPEN BABEL 2.3.1
ATOM    1  N   PHE     1       0.720   0.859  -0.499  1.00  0.00           N  
ATOM    2  C   PHE     1       0.760  -0.439   0.174  1.00  0.00           C  
ATOM    3  C   PHE     1       2.125  -1.161   0.111  1.00  0.00           C  
ATOM    4  O   PHE     1       2.253  -2.263   0.634  1.00  0.00           O  
ATOM    5  H   PHE     1       0.176   0.905  -1.352  1.00  0.00           H  
ATOM    6  H   PHE     1       0.585  -0.253   1.240  1.00  0.00           H  
ATOM    7  C   PHE     1      -0.336  -1.383  -0.373  1.00  0.00           C  
ATOM    8  C   PHE     1      -1.743  -0.858  -0.186  1.00  0.00           C  
ATOM    9  H   PHE     1      -0.200  -2.340   0.138  1.00  0.00           H  
ATOM   10  H   PHE     1      -0.145  -1.567  -1.440  1.00  0.00           H  
ATOM   11  C   PHE     1      -4.354   0.139   0.179  1.00  0.00           C  
ATOM   12  C   PHE     1      -2.316  -0.794   1.094  1.00  0.00           C  
ATOM   13  C   PHE     1      -2.504  -0.416  -1.277  1.00  0.00           C  
ATOM   14  C   PHE     1      -3.799   0.078  -1.100  1.00  0.00           C  
ATOM   15  C   PHE     1      -3.607  -0.301   1.276  1.00  0.00           C  
ATOM   16  H   PHE     1      -1.744  -1.138   1.954  1.00  0.00           H  
ATOM   17  H   PHE     1      -2.086  -0.476  -2.281  1.00  0.00           H  
ATOM   18  H   PHE     1      -4.373   0.412  -1.961  1.00  0.00           H  
ATOM   19  H   PHE     1      -4.033  -0.263   2.276  1.00  0.00           H  
ATOM   20  H   PHE     1      -5.362   0.519   0.320  1.00  0.00           H  
HETATM   21  C   ACE     1       0.873   2.036   0.208  1.00  0.00          
C  
HETATM   22  O   ACE     1       1.301   2.055   1.353  1.00  0.00          
O  
HETATM   23  C   ACE     1       0.484   3.302  -0.540  1.00  0.00          
C  
HETATM   24  H   ACE     1       1.253   4.060  -0.375  1.00  0.00          
H  
HETATM   25  H   ACE     1      -0.451   3.685  -0.116  1.00  0.00          
H  
HETATM   26  H   ACE     1       0.345   3.153  -1.616  1.00  0.00          
H  
HETATM   27  N   NME     1       3.115  -0.507  -0.549  1.00  0.00          
N  
HETATM   28  C   NME     1       4.474  -1.010  -0.616  1.00  0.00          
C  
HETATM   29  H   NME     1       5.163  -0.381  -0.040  1.00  0.00          
H  
HETATM   30  H   NME     1       4.474  -2.015  -0.195  1.00  0.00          
H  
HETATM   31  H   NME     1       4.822  -1.054  -1.654  1.00  0.00          
H  
HETATM   32  H   NME     1       2.906   0.422  -0.885  1.00  0.00          
H  
CONECT    1    5    2   21                                            
CONECT    2    1    7    3    6                                       
CONECT    2                                                           
CONECT    3   27    2    4                                            
CONECT    4    3                                                      
CONECT    5    1                                                      
CONECT    6    2                                                      
CONECT    7   10    8    9    2                                       
CONECT    7                                                           
CONECT    8   13    7   12                                            
CONECT    9    7                                                      
CONECT   10    7                                                      
CONECT   11   14   20   15                                            
CONECT   12    8   15   16                                            
CONECT   13   17   14    8                                            
CONECT   14   18   13   11                                            
CONECT   15   11   12   19                                            
CONECT   16   12                                                      
CONECT   17   13                                                      
CONECT   18   14                                                      
CONECT   19   15                                                      
CONECT   20   11                                                      
CONECT   21   23    1   22                                            
CONECT   22   21                                                      
CONECT   23   26   24   25   21                                       
CONECT   23                                                           
CONECT   24   23                                                      
CONECT   25   23                                                      
CONECT   26   23                                                      
CONECT   27   32   28    3                                            
CONECT   28   31   27   30   29                                       
CONECT   28                                                           
CONECT   29   28                                                      
CONECT   30   28                                                      
CONECT   31   28                                                      
CONECT   32   27                                                      
MASTER        0    0    0    0    0    0    0    0   32    0   32    0
END



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