[gmx-users] Heme group with CHARMM27 FF

[Sundar Jubilant]

 Dear Abraham,

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

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

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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