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 <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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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