[gmx-users] problem still there for ACE

[Justin Lemkul]

On 5/4/14, 3:06 PM, Albert wrote:
> Hello:
>
> I capped the protein with residues ACE and NMA at N-ter and C-ter respectively.
> Here is the coordinate:
>
> ATOM      1  CH3 ACE X  38       9.945  21.608  90.016  1.00 0.00           C
> ATOM      4 HH31HACE X  38      10.267  21.376  91.056  1.00 0.00           H
> ATOM      5 HH32HACE X  38       9.614  22.669  89.956  1.00 0.00           H
> ATOM      6 HH33HACE X  38       9.095  20.947  89.733  1.00 0.00           H
> ATOM      2  C   ACE X  38      11.113  21.380  89.058  1.00 0.00           C
> ATOM      3  O   ACE X  38      12.196  20.997  89.497  1.00 0.00           O
> ATOM      4  N   GLY X  39      10.957  21.602  87.705  1.00 0.00           N
> ATOM      5  CA  GLY X  39      12.077  21.382  86.795  1.00 0.00           C
> ATOM      6  C   GLY X  39      11.787  21.661  85.315  1.00 0.00           C
> ATOM      7  O   GLY X  39      12.527  21.182  84.455  1.00 0.00           O
>
> ....
>
> ATOM   2309  N   LYS X 335      38.981  11.135  41.177  1.00 0.00           N
> ATOM   2310  CA  LYS X 335      40.402  10.845  41.347  1.00 0.00           C
> ATOM   2311  C   LYS X 335      40.881  11.426  42.687  1.00 0.00           C
> ATOM   2312  O   LYS X 335      41.551  12.456  42.677  1.00 0.00           O
> ATOM   2313  CB  LYS X 335      41.191  11.366  40.117  1.00 0.00           C
> ATOM   2314  CG  LYS X 335      40.902  10.605  38.817  1.00 0.00           C
> ATOM   2315  CD  LYS X 335      41.781  11.075  37.647  1.00 0.00           C
> ATOM   2316  CE  LYS X 335      41.492  10.315  36.347  1.00 0.00           C
> ATOM   2317  NZ  LYS X 335      42.382  10.755  35.267  1.00 0.00           N1+
> 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
> END
>
>
>
> When I try to run command:
>
> pdb2gmx -f p.pdb -o gmx.pdb  -ter
>
> 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 LYS-335
>   0: COO-
>   1: COOH
>   2: CT2
>   3: 3TER
>   4: None
> 4
> End terminus LYS-335: None
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.5
> Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2top.c, line: 1109
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your
> coordinate file, add a new terminal database entry (.tdb), or select the proper
> existing terminal entry.
>
>
> When I run command:
>
> pdb2gmx -f p.pdb -o gmx.pdb
>
> Fatal error:
> atom N not found in buiding block 1ACE while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I noticed this thread:
> https://www.mail-archive.com/gmx-users@gromacs.org/msg49517.html
>
> and Justine said there is a N atom on ACE instead of the first atom of the next
> residue. However, as shown in my coordinate, there is NO atom N in ACE at all.
> And I cannot figure out what's the problem....
>

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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================