Re: [gmx-users] Heme group with CHARMM27 FF
Dear Abraham,
Sorry for making it hard. Since I am so new to this I guess I am not explaining
it clearly for you to help me.
First of all I dont want to ignore any hydrogens but as pdb2gmx was complaining
about my system and suggested me to add -ignh I did so.
My problem is how to update .hdb with heme hydrogen details.
So, here to follow your suggestion removing the hydrogen atoms I wish to ignore
I actually need to ignore the hydorgens in protein.
Thanks
Sundar
-Original Message-
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Fri, Apr 20, 2012 8:08 pm
Subject: Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 9:02 PM, Sundar Jubilant wrote:
Dear Abraham,
How would it work if I remove the hydrogen atoms that I
wish to ignore from my input co-ordinate file? The pdb2gmx
tries to add the missing hydorgen atoms for which the .hdb doesn't
have information.
You've never actually told us what hydrogens you want to ignore, so
you're making it hard to help you.
Mark
In my case here, I can consider heme as a ligand instead
of having it as protein since it doesn't need to be the part
of the protein.
Thanks for your information.
Sundar
-OriginalMessage-
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Fri, Apr 20, 2012 6:42 pm
Subject: Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 7:33 PM, Sundar Jubilant wrote:
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.
No, there is no ability to ignore them selectively - but
if you want to ignore any of them, you have to address the
heme hydrogen database issue, or go and remove the hydrogen atoms
that you wish to ignore from your input coordinate file.
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?
It's not a question of accuracy, but rather that if you
have bonded interactions between heme and protein, they have to
be part of the same [moleculetype], which is what pdb2gmx is
struggling to generate.
Mark
Thanks
Sundar
-Original Message-
From: Mark Abraham
To: Discussion list for GROMACS users
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 aspecific
problem. You'd like the ability tobuild hydrogen atoms
on a heme residue. pdb2gmxhas to have a specific recipe
for doing that.The manual describes the required format
and
Re: [gmx-users] Heme group with CHARMM27 FF
Dear Abraham, How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information. In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein. Thanks for your information. Sundar -Original Message- From: Mark Abraham To: Discussion list for GROMACS users Sent: Fri, Apr 20, 2012 6:42 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogenonly for pretein residues but not for the heme complexedwith it. No, there is no ability to ignore them selectively - but if you wantto ignore any of them, you have to address the heme hydrogendatabase issue, or go and remove the hydrogen atoms that you wish toignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. Howwould that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of thesame [moleculetype], which is what pdb2gmx is struggling togenerate. Mark Thanks Sundar -OriginalMessage- From: Mark Abraham To: Discussion list for GROMACS users 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: DearAbraham, 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 t
Re: [gmx-users] Heme group with CHARMM27 FF
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
To: Discussion list for GROMACS users
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 requestfor
help, else you'll just get told to go and read), but is unlikelyto 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 manualdescribes the required format and
gives an example. Someone's goingto 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, youdon't
need to re-generate them...
Mark
The error is
WARNING: atom HA is missing in residueHEM 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
-OriginalMessage-
From: Mark Abraham
To: Discussion list for GROMACS users
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 blo
Re: [gmx-users] Heme group with CHARMM27 FF
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 pdbfile 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 To: Discussion list for GROMACS users 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 havereceived 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gro
[gmx-users] Heme group with CHARMM27 FF
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 . 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? Thanks, Sundar Jubilant -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
