[gmx-users] help regarding pull code
Hi I am trying to understand the pull code with the tutorial i found from here. http://www.csc.fi/chem/course/gmx2007/ i have a confusion about it. when i put one atom in the reference group and the other atom in the group_1, doesn't it mean that, the pulling should be in one direction? But the result i am getting, it looks like it is pulled in both way. and if I wanted to pull with a group of atom, should I just put the atoms in group_2, group_3, in this manner? can any one help me with this? Thanks in advance. Tawhid ___ 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] pdb2gmx error
I am sorry, my previous mail bounced back, as it was over 50 KB.
I changed the ffG43a1 to include the GTP and GDP which I got from a previous
post here. {http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html}
I changed some structure like giving comment with ; as the origicanal # was
giving error. but now it tells me there is an error that 05* is not found in
the atom type database.
Program pdb2gmx, VERSION 3.3.1
Source code file: resall.c, line: 148
Fatal error:
Atom type O5* (residue GTP) not found in atomtype database
---
I am including the file here .the GTP residue is at the bottom of the file.
https://netfiles.uiuc.edu/tezaz2/shared/ffG43a1.rtp
Is there any other GTP and GDP residue for the force field 43a1?
Thanks in advance.
Tawhid
- Original Message
From: Justin A. Lemkul <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Monday, November 26, 2007 9:14:37 PM
Subject: Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz <[EMAIL PROTECTED]>:
> Thanks a lot Justin. It worked really nice.
>
> now I am stuck with another problem. I need to add the Building block
GTP and
> GDP in 43a1, as I need to get the topology of a tubulin monomer. I
got the
> file from a old post here.
>
> http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html
>
> I copied and pasted it into my file, yet, as the structure doesn't
match it
> gave several errors.
>
> is there any way to fix this?
That depends entirely upon what your errors are and what you're trying
to do.
Please provide more details.
-Justin
>
> Thanks a lot for your help.
>
> Tawhid
>
>
>
> - Original Message
> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users
> Sent: Monday, November 26, 2007 7:14:43 PM
> Subject: Re: [gmx-users] pdb2gmx error
>
>
> Quoting Tawhid Ezaz <[EMAIL PROTECTED]>:
>
> > Hi,
> >
> > I have just started to learn gromacs. I am facing a problem to make
> topology
> > file of a myoglobin. I got the pdb file from the csc tutorial.
> >
> > When i am running the pdb2gmx with
> >
> > pdb2gmx -f conf.pdb -p topol.top
> >
> > i get the message, HEME148 CAB1428 0.569
> > HEME148 CAC1437 0.562 0.820
> > N-terminus: NH3+
> > C-terminus: COO-
> > Now there are 148 residues with 1451 atoms
> > ---
> > Program pdb2gmx, VERSION 3.3.1
> > Source code file: pdb2top.c, line: 570
> >
> > Fatal error:
> > atom N not found in residue 1ACE while combining tdb and rtp
> > ---
> >
> > I was using 43a1 force field (0), {but none of them works}.
> >
> > i read some previous post and got the idea that there should be a N
> atom with
> > should be linked with ACE, but my conf.pdb files does not have any.
I
> have
> > topol.top file from the tutorial but didn't show how I can generate
> that.
>
> Use the -ter option with pdb2gmx, and select 'none' when prompted.
> That way,
> pdb2gmx does not look for an N-terminal nitrogen (which is obviously
> absent in
> an acetyl group).
>
> -Justin
>
> >
> > I am a totally newbie, thus I am wondering what should I do. Which
> file I
> > should correct to get rid of those? Do I need to know the bonding
of
> every
> > atom in the molecule for that?
> >
> > Thanks in advance
> >
> > Tawhid
> >
> >
> >
> >
> >
>
>
>
>
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
>
> ___
> 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
>
>
>
>
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
___
Re: [gmx-users] pdb2gmx error
Thanks a lot Justin. It worked really nice.
now I am stuck with another problem. I need to add the Building block GTP and
GDP in 43a1, as I need to get the topology of a tubulin monomer. I got the
file from a old post here.
http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html
I copied and pasted it into my file, yet, as the structure doesn't match it
gave several errors.
is there any way to fix this?
Thanks a lot for your help.
Tawhid
- Original Message
From: Justin A. Lemkul <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Monday, November 26, 2007 7:14:43 PM
Subject: Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz <[EMAIL PROTECTED]>:
> Hi,
>
> I have just started to learn gromacs. I am facing a problem to make
topology
> file of a myoglobin. I got the pdb file from the csc tutorial.
>
> When i am running the pdb2gmx with
>
> pdb2gmx -f conf.pdb -p topol.top
>
> i get the message, HEME148 CAB1428 0.569
> HEME148 CAC1437 0.562 0.820
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 148 residues with 1451 atoms
> ---
> Program pdb2gmx, VERSION 3.3.1
> Source code file: pdb2top.c, line: 570
>
> Fatal error:
> atom N not found in residue 1ACE while combining tdb and rtp
> ---
>
> I was using 43a1 force field (0), {but none of them works}.
>
> i read some previous post and got the idea that there should be a N
atom with
> should be linked with ACE, but my conf.pdb files does not have any. I
have
> topol.top file from the tutorial but didn't show how I can generate
that.
Use the -ter option with pdb2gmx, and select 'none' when prompted.
That way,
pdb2gmx does not look for an N-terminal nitrogen (which is obviously
absent in
an acetyl group).
-Justin
>
> I am a totally newbie, thus I am wondering what should I do. Which
file I
> should correct to get rid of those? Do I need to know the bonding of
every
> atom in the molecule for that?
>
> Thanks in advance
>
> Tawhid
>
>
>
>
>
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
___
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___
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Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] pdb2gmx error
Hi,
I have just started to learn gromacs. I am facing a problem to make topology
file of a myoglobin. I got the pdb file from the csc tutorial.
When i am running the pdb2gmx with
pdb2gmx -f conf.pdb -p topol.top
i get the message, HEME148 CAB1428 0.569
HEME148 CAC1437 0.562 0.820
N-terminus: NH3+
C-terminus: COO-
Now there are 148 residues with 1451 atoms
---
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 570
Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---
I was using 43a1 force field (0), {but none of them works}.
i read some previous post and got the idea that there should be a N atom with
should be linked with ACE, but my conf.pdb files does not have any. I have
topol.top file from the tutorial but didn't show how I can generate that.
I am a totally newbie, thus I am wondering what should I do. Which file I
should correct to get rid of those? Do I need to know the bonding of every atom
in the molecule for that?
Thanks in advance
Tawhid
___
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
