[gmx-users] problem still there for ACE

[Justin Lemkul]

On 5/5/14, 12:30 AM, Albert wrote:
> 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
> -------------------------------------------------------
>

CHARMM has unique nomenclature for amide H atoms, so H needs to be renamed HN, 
though unfortunately that's also wrong in the .rtp file.  I'll fix that for the 
future.

>
> 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
>

If you use -ignh, you'll be ignoring the 4 H atoms on NMA, and since there is no 
NMA in the .hdb file, they're not rebuilt and remain missing.  The simplest 
thing to do is rename your amide H atom and fix the .rtp file.  I'll fix the 
.hdb for a future release.

-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

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