Re: [gmx-users] On posre.itp
On 7/05/2011 7:16 PM, Mr Bernard Ramos wrote:
Thanks for the response. I will be doing a simple MD
without the positional restraints. How do I go about reviewing the
code for posres? What I did was to add new ff parameters for a new
residue I introduced. May I please know what file in the
program determines the posres so that I can revew them. Thanks.
Please give full descriptions the first time. I posted a noob question
on the AMBER mailing list a few months back, and would never have gotten
the problem solved except that I included some details that I thought
were irrelevant, and someone spotted my problem. We've all got better
things to do than play question-and-answer. You might have invented some
atom names that pdb2gmx doesn't know how to cope with - but you haven't
said whether your apparently erronously generated position restraints
are specific to your new residue or not. Unfortunately you haven't
shared your atom names after I suggested the atom names were probably
the problem, and I'm not going to make guesses. There's various
databases in $GMXLIB/share/top for various force fields, but I don't
know your GROMACS version either...
I don't think looking at the code will lead to a solution.
Mark
--- On *Sat, 5/7/11, Mark Abraham //* wrote:
From: Mark Abraham
Subject: Re: [gmx-users] On posre.itp
To: "Discussion list for GROMACS users"
Date: Saturday, May 7, 2011, 5:10 PM
On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote:
Hi everyone!
I was able to generate a pdb file in which the hydrogens for the
molecule are already included (that way I avoided using the hdb
file for the pdb2gmx). However, when I checked the posre.itp, the
some of the restraints were applied to the hydrogens. Is this
correct because I am not sure since I what I know is that the
restraints should be applied to heavy atoms.
Maybe your atom names are confusing pdb2gmx. Maybe you're
comparing apples and oranges with the indices in the coordinate
file and the indices in the posres.itp (which are relative to the
[atoms], IIRC).
Are the positional restraints needed only for the equalibration
step but not for the production runs in normal MD simulations.
Thanks.
Up to you. Do you want to sample under unphysical restraints or not?
Mark
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Re: [gmx-users] On posre.itp
I think I've got the answer. It is on the input pdb file. The heavy atoms need to be labeled properly. thanks --- On Sat, 5/7/11, Mr Bernard Ramos wrote: From: Mr Bernard Ramos Subject: Re: [gmx-users] On posre.itp To: "Discussion list for GROMACS users" Date: Saturday, May 7, 2011, 5:16 PM Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks. --- On Sat, 5/7/11, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] On posre.itp To: "Discussion list for GROMACS users" Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-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 -Inline Attachment Follows- -- gmx-users mailing list gmx-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-- 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
Re: [gmx-users] On posre.itp
Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks. --- On Sat, 5/7/11, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] On posre.itp To: "Discussion list for GROMACS users" Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-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-- 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
Re: [gmx-users] On posre.itp
On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? 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...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] On posre.itp
Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. -- 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
