[gmx-users] Generating topology for a HEM protein with CHARMM27
Justin Lemkul
jalemkul at vt.edu
Thu May 26 03:01:43 CEST 2016
On 5/25/16 9:58 AM, zeineb SI CHAIB wrote:
> @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?
>
SG is an atom *name*, not an atom *type*.
atomtypes.atp is also irrelevant anyway, as it is only read by pdb2gmx, so
that's not how you add new atom types. But in any case, this is not what you
should be doing anyway. Be careful that your protonation states are correct -
make sure that -SH is correct (instead of the thiolate form) before adding a
bunch of parameters and trying to do the simulation.
-Justin
> 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.
>
>
--
==================================================
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
==================================================
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