[gmx-users] Generating topology for a HEM protein with CHARMM27

[zeineb SI CHAIB]

@Justin, 

Thank you very much for your help, I finally fixed the problem but I'm having another one with grompp (which was expected): The error that I get is: 

ERROR 7 [file topol.top, line 41571]:
  No default Proper Dih. types

Fatal error:
There were 13 errors in input file(s)

I think that the problem is about the bond parameters between SH in cystein and HEME iron group, isn't it? 

After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file ffbonded.it:




	
	
	
	
[
bondtypes ]
;
i	j	   func	b0	 kb
  SG
  FE        1      0.232  209200.0




[
angletypes ]
;
i	j	k	func	th0	cth	ub0	cub
CT2
   SG       FE       5      100.6   418.4   0.0     0.0
SG
    FE       NPH      5       90.0   836.8   0.0     0.0
SG
    FE       NPH      5       90.0   836.8   0.0     0.0
SG
    FE       NPH      5       90.0   836.8   0.0     0.0
SG
    FE       NPH      5       90.0   836.8   0.0     0.0

;
###
X	
 CS	    SS	X	  9	    0.20	0.0	3

CA
     CB      SG      FE      9       0.20    0.0   3
HB1
    CB      SG      FE      9       0.20    0.0   3
HB1
    CB      SG      FE      9       0.20    0.0   3

;
###
X	
 FE	    SS	X	  9	    0.00	0.0	  4
CB
     SG      FE      NPH     9       0.00    0.0     4
CB
     SG      FE      NPH     9       0.00    0.0     4
CB
     SG      FE      NPH     9       0.00    0.0     4







But after that, I had another type of error:

Fatal error:
Unknown bond_atomtype SG






I added an SG entry in atomtypes.atp but I'm having the same error? Am I missing something? 

Thank you very much for all your help and guidance Justin!

Regards. 

Zeineb.  



From: zeineb-14 at hotmail.com
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Generating topology for a HEM protein with CHARMM27
Date: Mon, 23 May 2016 10:31:05 +0100




I'm looking to generate the topology of a HEM protein , I choose CHARMM as a force field. At the begining, when I run pdb2gmx I had this error about missing hydrogen's:

WARNING:
atom HA is missing in residue HEM 473 in the pdb file

        You
might need to add atom HA to the hydrogen database of building block
HEME

        in
the file aminoacids.hdb (see the manual)






WARNING:
atom HB is missing in residue HEM 473 in the pdb file

        You
might need to add atom HB to the hydrogen database of building block
HEME

        in
the file aminoacids.hdb (see the manual)









-------------------------------------------------------
Program
pdb2gmx, VERSION 4.6.5
Source
code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line:
1588



Fatal
error:
There
were 30 missing atoms in molecule Other2, 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
-------------------------------------------------------
After a research, I found what was missing: I made a copy of aminoacids.hdb (Charmm27.ff folder) in my working directory and I edited this file: 
I added the following Lines: 




	
	
	
	



HEME 16 

1
      1       HA
     CHA     C1A     C4D
1
      1       HB
     CHB     C4A     C1B
1
      1       HC
     CHC     C1C     C4B
1
      1       HD
     CHD     C1D     C4C
3
      4       HMA
    CMA     C3A     C2A
2
      6       HAA
    CAA     C2A
    CBA
2
      6       HBA
    CBA     CAA
    CGA
3
      4       HMB
    CMB     C2B     C1B
1
      1       HAB
    CAB     C3B     CBB
2
      3       HBB
    CBB     CAB     C3B
3
      4       HMC
    CMC     C2C     C1C
1
      1       HAC
    CAC     CBC     C3C
2
      3       HBC
    CBC     CAC     C3C
3
      4       HMD
    CMD     C2D     C1D
2
      6       HAD
    CAD     C2D     CBD
2
      6       HBD
    CBD     CAD     CGD



I fixed the problem of missing hydrogens but I'm having another type of error:

Special Atom Distance matrix:
                  HEM360  HEM360
                    CAB2    CAC3
  HEM360    CAC3   0.796
  HEM360    FE43   0.557   0.557

-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1.2
Source code file: /home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, line: 645

Fatal error:
Residue 'HEM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

I added an entry in residuetype.dat (HEM      Protein), after making a copy in my working directory but it didn't fix the problem. I verified each file and they seem OK, I can't find where is the problem!!! Any help please!!!

Kind regards. 

Zeineb.