[gmx-users] Prot_prep_query
Hi, Thanks for your suggestions. I was using the 0 option gromos FF in pdb2gmx. As you said the behavior is strange. However i found a fix. I was using a 2 step procedure 1) strip hydrogen > output pdb 2) input pdb > write output pdb with -inter flag instead i used 1) strip hydrogen > output pdb 2) input pdb > write pdb gro top using -inter flag (gro has hydrogens, pdb does not) 3) use gro as input > take pdb output (pdb has hydrogens) Thanks Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Prot_prep_query
Hi Prasenjit,
First, please don't include a whole digest into your reply :S What a
scroll down.
Did pdb2gmx say anything when not giving hydrogen atoms? It sounds
weird that they were added in the .top but not in the .itp. Maybe
first clean the directory, such that you only have the original .pdb
and run pdb2gmx with -ignh but without -inter. If you find that the
output .pdb/.gro file doesn't have the hydrogens in, but the .top file
does, please report back exactly what command you gave, which force
field, which operating system and which shoe size you have. Well, you
can leave the latter. The output of pdb2gmx might come in handy.
Best,
Tsjerk
On 4/11/07, pkmukher <[EMAIL PROTECTED]> wrote:
Hello Andrea,
Thanks for your reply. Actually I am not doing a NMR
constraint based refinement of the structure. Its a NMR
derived ligand-protein complex submitted in the pdb. I want
to prepare the complex using the tutorial. In the tutorial
they have a crystal structure without hydrogens. Since in my
case I had hydrogens present and it was interfering with the
preparation using gromos ff i thought of stripping the
hydrogens and re adding them. I thought of using the -inter
flag to control the protonation of key residue types. My
problem is that when used the stripped pdb in the second
stage the output pdb file does not write the hydrogens while
the top file does. Since the next step will be to add the
ligand coordinates(polar hydrogens added) I should also have
a protein pdb structure with polar hydrogens added.Thanks
**In case you need to refer to the previous mail
Hello gromacs users,
I am facing a particular problem in the preparation of my
protein.I have a NMR derived structure with hydrogens. To
prepare my protein i thought of a two step procedure
1)stripping the protein of the hydrogens using -ignh and
saving pdb output
2)submitting the pdb output file from stage 1 using the
-inter flag to get my final .top .gro and .pdb files
I find that at the end of step 1 the pdb output is stripped
of hydrogens.
In the second stage I find that the .top file has the
hydrogens listed (only polar hydrogens) but the pdb output
is still without any hydrogens.
I want to follow the gromacs tutorial titled
GROMACS Tutorial for Drug – Enzyme Complex.
http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
here they have used a prepared protein pdb file while
merging the ligand coordinates to form the final complex.
My questions are
1) why the pdb file written in step two does not contain the
hydrogens and how can i solve this issue?
2) Is there any other way to prepare the ligand-protein
complex without using the protein .pdb output?
3) This is a slightly unrelated question. Could some body
guide me to any tutorials etc where they have shown how to
calculate gausssian charges for the ligand and then
incorporate into the gromacs ligand file?
I can provide the protein structure file. I couldnt load it
to the group mail because of size limitations
Thanking you in anticipation
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help'
> to
> [EMAIL PROTECTED]
>
> You can reach the person managing the list at
> [EMAIL PROTECTED]
>
> When replying, please edit your Subject line so it is more
> specific than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: overcome the integration problem (installing
> CVS) (Yang Ye)
>2. Re: overcome the integration problem (installing
> CVS)
> (David van der Spoel)
>3. Re: question about the total-energy of energy
> minimization
> (Mark Abraham)
>4. Hi all (ann rose)
>5. Re: overcome the integration problem (installing
> CVS) (Berk Hess)
>6. Re: Hi all (Mark Abraham)
>7. Prot_prep_problem (pkmukher)
>8. Re: Prot_prep_problem (andrea spitaleri)
>
>
> --
>
>
> Message: 1
> Date: Wed, 11 Apr 2007 18:07:19 +0800
> From: Yang Ye <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] overcome the integration problem
> (installing
> CVS)
> To: Discussion list for GROMACS users
> Message-ID:
> <[EMAIL PROTECTED]> Content-Type: text/plain;
> charset=ISO-8859-1; format=flowed
>
>
>
> On 4/11/2007 5:52 PM, Dr Itamar Kass wrote:
> > Shalom all,
> >
> > To my best understanding, there is a correction to the
> > single precision integration problem ("A common,
> > avoidable source of error in molecular dynamics
> > integrators" J. Chem. Phys. 126, 046101 (2007).) at the
> CVS. >
> > I want to know were can I get it and how to install it.
> > First, the GROMACS site is down now. Second from the bit
> > I have read, it is not clear to me how to install the
> stable CVS and not an experimentally version. >
> >
> Stable version:
> cvs -z3 -d :pserver:[EMAIL PROTECTED]
[gmx-users] Prot_prep_query
Hello Andrea,
Thanks for your reply. Actually I am not doing a NMR
constraint based refinement of the structure. Its a NMR
derived ligand-protein complex submitted in the pdb. I want
to prepare the complex using the tutorial. In the tutorial
they have a crystal structure without hydrogens. Since in my
case I had hydrogens present and it was interfering with the
preparation using gromos ff i thought of stripping the
hydrogens and re adding them. I thought of using the -inter
flag to control the protonation of key residue types. My
problem is that when used the stripped pdb in the second
stage the output pdb file does not write the hydrogens while
the top file does. Since the next step will be to add the
ligand coordinates(polar hydrogens added) I should also have
a protein pdb structure with polar hydrogens added.Thanks
**In case you need to refer to the previous mail
Hello gromacs users,
I am facing a particular problem in the preparation of my
protein.I have a NMR derived structure with hydrogens. To
prepare my protein i thought of a two step procedure
1)stripping the protein of the hydrogens using -ignh and
saving pdb output
2)submitting the pdb output file from stage 1 using the
-inter flag to get my final .top .gro and .pdb files
I find that at the end of step 1 the pdb output is stripped
of hydrogens.
In the second stage I find that the .top file has the
hydrogens listed (only polar hydrogens) but the pdb output
is still without any hydrogens.
I want to follow the gromacs tutorial titled
GROMACS Tutorial for Drug Enzyme Complex.
http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
here they have used a prepared protein pdb file while
merging the ligand coordinates to form the final complex.
My questions are
1) why the pdb file written in step two does not contain the
hydrogens and how can i solve this issue?
2) Is there any other way to prepare the ligand-protein
complex without using the protein .pdb output?
3) This is a slightly unrelated question. Could some body
guide me to any tutorials etc where they have shown how to
calculate gausssian charges for the ligand and then
incorporate into the gromacs ligand file?
I can provide the protein structure file. I couldnt load it
to the group mail because of size limitations
Thanking you in anticipation
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help'
> to
> [EMAIL PROTECTED]
>
> You can reach the person managing the list at
> [EMAIL PROTECTED]
>
> When replying, please edit your Subject line so it is more
> specific than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: overcome the integration problem (installing
> CVS) (Yang Ye)
>2. Re: overcome the integration problem (installing
> CVS)
> (David van der Spoel)
>3. Re: question about the total-energy of energy
> minimization
> (Mark Abraham)
>4. Hi all (ann rose)
>5. Re: overcome the integration problem (installing
> CVS) (Berk Hess)
>6. Re: Hi all (Mark Abraham)
>7. Prot_prep_problem (pkmukher)
>8. Re: Prot_prep_problem (andrea spitaleri)
>
>
> --
>
>
> Message: 1
> Date: Wed, 11 Apr 2007 18:07:19 +0800
> From: Yang Ye <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] overcome the integration problem
> (installing
> CVS)
> To: Discussion list for GROMACS users
> Message-ID:
> <[EMAIL PROTECTED]> Content-Type: text/plain;
> charset=ISO-8859-1; format=flowed
>
>
>
> On 4/11/2007 5:52 PM, Dr Itamar Kass wrote:
> > Shalom all,
> >
> > To my best understanding, there is a correction to the
> > single precision integration problem ("A common,
> > avoidable source of error in molecular dynamics
> > integrators" J. Chem. Phys. 126, 046101 (2007).) at the
> CVS. >
> > I want to know were can I get it and how to install it.
> > First, the GROMACS site is down now. Second from the bit
> > I have read, it is not clear to me how to install the
> stable CVS and not an experimentally version. >
> >
> Stable version:
> cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs
> login cvs -z3 -d
> :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r
> release-3-3-patches gmx
>
> HEAD Branch
> cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs
> login cvs -z3 -d
> :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx
>
> > Best,
> > Itamar
> >
> > ---
> >
> > "Prediction is very difficult, especially about the
> future" - Niels Bohr >
> >
===
> > | Itamar Kass, Ph.D.
> > | Postdoctoral Research Fellow
> > |
> > |Molecular Dynamics Group
> > | School of Molecular and Microbial Sciences (SMMS)
> > | Chemistry Building (#68)
> > | The University of Queensland
> > | St. Lucia Campus, Brisbane, QLD 4067
> > | Australia
> > |
> > | Tel
