[gmx-users] Heme group with CHARMM27 FF

Fri Apr 20 11:33:35 CEST 2012

 Dear Abraham,

I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it.

One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation?

Thanks
Sundar

-----Original Message-----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Fri, Apr 20, 2012 3:57 pm
Subject: Re: [gmx-users] Heme group with CHARMM27 FF

              On 20/04/2012 4:38 PM, Sundar Jubilant wrote:    

 Dear Abraham,

              Thanks for your email. I have already read the manual to              solve the problem but I wasn't successful.

    That's good to say (particularly the first time you post a request    for help, else you'll just get told to go and read), but is unlikely    to get much help because you haven't identified a specific problem.    You'd like the ability to build hydrogen atoms on a heme residue.    pdb2gmx has to have a specific recipe for doing that. The manual    describes the required format and gives an example. Someone's going    to have to do some work.

              I need little more detailed answer to solve the problem. 

              By the way, here is the full command line for which I got              the error.

              $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top              -i CYP_CHARMM.itp -ignh

    If you don't ignore hydrogens, and they're already correct, you    don't need to re-generate them...

    Mark

              The error is

            WARNING: atom HA is missing in residue                    HEM 513 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 513 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)

                    WARNING: atom HC is missing in residue HEM 513 in                    the pdb file
                             You might need to add atom HC to the                    hydrogen database of building block HEME
                             in the file aminoacids.hdb (see the manual)

                    .
                    .
                    .
                    .
                    .
-------------------------------------------------------
                    Program pdb2gmx, VERSION 4.5.3
                    Source code file: pdb2top.c, line: 1449

                    Fatal error:
                    There were 30 missing atoms in molecule Protein, 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
-------------------------------------------------------

                    Thanks.

                    Sundar Jubilant

-----Original            Message-----
            From: Mark Abraham <Mark.Abraham at anu.edu.au>
            To: Discussion list for GROMACS users            <gmx-users at gromacs.org>
            Sent: Fri, Apr 20, 2012 2:17 pm
            Subject: Re: [gmx-users] Heme group with CHARMM27 FF

              On 20/04/2012 2:33 PM, Sundar Jubilant wrote:              
Dear                      gmx-users,

                      I am new to Gromacs and trying to simulate a                      protein with a heme group using CHARMM27 ff in                      Gromacs 4.5.3. I have received the following error                      while running pdb2gmx .

              When asking for help, please give your full command lines              and/or interactive selections so that we can know more              context.

                      WARNING: atom HA is missing in residue HEM 513 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 513 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)

                      WARNING: atom HC is missing in residue HEM 513 in                      the pdb file
                               You might need to add atom HC to the                      hydrogen database of building block HEME
                               in the file aminoacids.hdb (see the                      manual)

                      .
                      .
                      .
                      .
                      .
-------------------------------------------------------
                      Program pdb2gmx, VERSION 4.5.3
                      Source code file: pdb2top.c, line: 1449

                      Fatal error:
                      There were 30 missing atoms in molecule Protein,                      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
-------------------------------------------------------

                      Can anyone help how can I generate and add                      hydrogen database information for heme to be used                      with CHARMM27 ff?

                    You'll have to read the applicable sections of                    manual chapter 5, make a local copy of the                    charmm27.ff folder in your working directory and                    editing aminoacids.hdb to add the generation                    information. When you're done, please post your                    efforts so that others might be able to benefit from                    them in future. (Also, search first in case this has                    already happened!)

                    Mark

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