[gmx-users] pdb2gmx error with addition of terminal group

[Justin Lemkul]

On 7/8/15 6:39 AM, anu chandra wrote:
> Dear Gromacs users,
>
> I am trying to use pdb2gmx tool to generate topology for my membrane
> protein system with chamrm36 force field. I have downloaded Gromacs
> compatible Chamrmm36ff from
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the
> N-terminal acetyl (ACE) and  C-terminal N-methyl amide (NMA) group attached
> to the respective terminals. As shown below, I have named the residue/atom
> names according to the one present in 'merged.rtp' in the charmm36ff file.
>
> *******************************************************************************
> ATOM      1  CH3 ACE     1      37.718  66.293  67.509  1.00  0.00      PROA
> ATOM      2 HH31 ACE     1      36.850  66.906  67.178  1.00  0.00      PROA
> ATOM      3 HH32 ACE     1      37.393  65.240  67.617  1.00  0.00      PROA
> ATOM      4 HH33 ACE     1      38.522  66.381  66.751  1.00  0.00      PROA
> ATOM      5  C   ACE     1      38.195  66.802  68.805  1.00  0.00      PROA
> ATOM      6  O   ACE     1      37.657  67.757  69.352  1.00  0.00      PROA
> ATOM      7  N   VAL     1      39.245  66.166  69.366  1.00  0.00      PROA
> ATOM      8  HN  VAL     1      39.698  65.409  68.911  1.00  0.00      PROA
> ATOM      9  CA  VAL     1      39.818  66.600  70.628  1.00  0.00      PROA
> ATOM     10  HA  VAL     1      39.044  66.557  71.385  1.00  0.00      PROA
> ------------------------------------
> ------------------------------------
> ATOM   2599  HG1 SER   165      47.684  67.280  81.712  1.00  0.00      PROA
> ATOM   2600  C   SER   165      46.288  64.682  84.443  1.00  0.02      PROA
> ATOM   2601  O   SER   165      46.621  64.090  85.417  1.00  0.04      PROA
> ATOM   2602  N   NMA   166      45.020  64.893  84.635  1.00  0.03      PROA
> ATOM   2603  HN  NMA   166      44.986  65.779  85.049  1.00  0.00      PROA
> ATOM   2604  CH3 NMA   166      44.322  63.814  85.342  1.00  0.04      PROA
> ATOM   2605 HH31 NMA   166      44.694  62.798  85.066  1.00  0.04      PROA
> ATOM   2606 HH32 NMA   166      43.284  63.888  85.004  1.00  0.04      PROA
> ATOM   2607 HH33 NMA   166      44.382  63.845  86.467  1.00  0.06      PROA
> ***********************************************************************************
>
> But, when running ' gmx pdb2gmx -f  input.pdb -ter' and opting 'none' for
> the terminal, the pogram terminate with following error
>
> ***********************************************************************************
> Back Off! I just backed up topol.top to ./#topol.top#
> Processing chain 1 (2607 atoms, 167 residues)
> Identified residue ACE1 as a starting terminus.
> Warning: Residue NMA166 in chain has different type (Other) from starting
> residue ACE1 (Protein).
> Identified residue SER165 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                     CYS64   CYS72   CYS95  MET100  CYS101
>                    SG1007  SG1123  SG1473  SD1554  SG1568
>     CYS72  SG1123   0.857
>     CYS95  SG1473   2.147   1.806
>    MET100  SD1554   2.390   1.830   0.806
>    CYS101  SG1568   1.896   1.488   0.334   0.773
>    MET143  SD2232   1.844   1.750   1.858   2.389   1.687
> Select start terminus type for ACE-1
>   0: NH3+
>   1: NH2
>   2: 5TER
>   3: None
> 3
> Start terminus ACE-1: None
> Select end terminus type for SER-165
>   0: COO-
>   1: COOH
>   2: CT2
>   3: 3TER
>   4: None
> 4
> End terminus SER-165: None
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.4
> Source code file:
> /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091
>
> 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.*
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> **************************************************************************************
>
> Can anybody help me to figure out what is wrong with my input pdb file?
>

Note that pdb2gmx finds Ser instead of NMA as the last residue.  The clue is:

" Warning: Residue NMA166 in chain has different type (Other) from starting 
residue ACE1 (Protein)"

You need to add NMA as "Protein" in residuetypes.dat.  You don't want a 
non-patched terminus on Ser, you want a non-patched terminus on NMA.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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