[gmx-users] problem still there for ACE

[Albert]

On 05/04/2014 11:44 PM, Justin Lemkul wrote:
> No, what I said in that thread is that the OP had constructed ACE 
> incorrectly such that it contained an N that shouldn't be there. There 
> should indeed not be any N atom in ACE.  The second approach is simply 
> incorrect; you need to interactively select termini when using capping 
> groups.  The first approach was completely correct, but note that the 
> problem is not with ACE, it is with NMA. pdb2gmx is finding LYS as the 
> terminus instead of NMA, and when you tell pdb2gmx to apply to 
> terminus, LYS has a dangling (incomplete) end.  Likely this stems from 
> the fact that residuetypes.dat does not, by default, include NMA as a 
> Protein residue, so pdb2gmx finds a Protein chain from ACE38 - LYS335, 
> then a separate Other chain of NMA.  Adding NMA to residuetypes.dat 
> and repeating the first approach will solve the problem.
>
> -Justin


HI Justin:

thanks a lot for helpful advices.

I add NMA to residuetypes.dat. and run it again:


pdb2gmx -f p.pdb -o gmx.pdb -ter

Linking CYS-121 SG-624 and CYS-198 SG-1215...
Select start terminus type for ACE-38
  0: NH3+
  1: NH2
  2: 5TER
  3: None
3
Start terminus ACE-38: None
Select end terminus type for NMA-335
  0: COO-
  1: COOH
  2: CT2
  3: 3TER
  4: None
4
End terminus NMA-335: None
Opening force field file 
/soft/gromacs-4.6.5/share/gromacs/top/charmm36-mar2014.ff/merged.arn

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.5
Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2gmx.c, line: 727

Fatal error:
Atom HN in residue NMA 335 was not found in rtp entry NMA with 6 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


Here is a coordinate for NMA:

ATOM   4782  N   NMA X 335      40.573  10.815  43.885  1.00 
0.00           N
ATOM   4784  H   NMA X 335      40.023   9.969  43.894  1.00 
0.00           H
ATOM   4783 CH3  NMA X 335      41.042  11.390  45.138  1.00 
0.00           C
ATOM   4785 HH31 NMA X 335      41.625  12.311  44.913  1.00 
0.00           H
ATOM   4786 HH32 NMA X 335      40.172  11.644  45.784  1.00 
0.00           H
ATOM   4787 HH33 NMA X 335      41.688  10.657  45.670  1.00 
0.00           H

which is consistent from that in merge.rtp file:
[ NMA ] ; terminal residue, provided by Mark Abraham
  [ atoms ]
        N       NH1     -0.470  1
        H       H       0.310   1
        CH3     CT3     -0.110  1
        HH31    HA3     0.090   1
        HH32    HA3     0.090   1
        HH33    HA3     0.090   1
  [ bonds ]
        -C      N
        N       H
        N       CH3
        CH3     HH31
        CH3     HH32
        CH3     HH33
  [ impropers ]
        N       -C      CH3     H
        -C      CH3     N       -O






I don't know why it claimed error again.... I try to run:

pdb2gmx -f p.pdb -o gmx.pdb -ter -ign

but it failed with messages:

Fatal error:
There were 4 missing atoms in molecule Protein_chain_X, if you want to 
use this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



thanks a lot