The error itself is self explanatory, there are no 22 atoms in your protein
structure, that suppose to be there. If you want to ignore those atoms when you
build your topology you can use the "-missing" option when you run pdb2gmx. But
if you need all the atoms you better construct a complete pr
Dear all gromacs users,
While i am running gromacs software i am getting following error.Let me
know that error how to over come.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology.
Suryanarayana Seera,
PhD student,
Hyderabad,
I
Dear Chris
Thanks again for your reply.
On Sat, Jun 2, 2012 at 10:52 PM, Christopher Neale <
chris.ne...@mail.utoronto.ca> wrote:
> I suspect that you can find an equation to relate the surface tension to
> the ratio of the pressure along z to the pressure along xy that is required
> to maintai
Dear Gromacs experts,
I am planing to use tabulated potentials
for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] ,
Here 1<= n <= 3 . I have three different K values (i.e K1,K2,K3 ) one for
each 'n' value ( Here 'n' is multiplicity). I have
OK, we find the bug. several words have problem of Uppercase and lowercase.
thank you very much!
--- 12年6月3日，周日, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] Atomtype 1
收件人: "Discussion list for GROMACS users"
日期: 2012年6月3日,周日,下午9:19
On 6/3/12 9:16 AM, xi zhao wrote:
Hi,
You may also need to name your terminal DNA residues appropriately in
your pdb file, as for the AMBER force fields the terminal DNA residues
are named differently. Check out the dna.rtp file for these naming
conventions.
Cheers
Tom
On 03/06/12 14:50, Justin A. Lemkul wrote:
On 6/3/1
there were two atoms that were new , i provided them in the .rtp file. only
then i ran the command
regards
ram
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Re-dangling-bond-at-at-one-of-the-terminal-ends-tp4998029p4998031.html
Sent from the GROMACS Users Forum mailing l
On 6/3/12 9:47 AM, ramaraju801 wrote:
HI, everyone
am working on a system consisting of protein-DNA complex,where an protein
comes and binds to the DNA to form a complex. To produce an topology file in
gromacs i gave the command " pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter
-ignh -ff amber9
HI, everyone
am working on a system consisting of protein-DNA complex,where an protein
comes and binds to the DNA to form a complex. To produce an topology file in
gromacs i gave the command " pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter
-ignh -ff amber99 " .
its creating the topology files of
On 6/3/12 9:37 AM, xi zhao wrote:
in windows , I use ultraedit, in linux ,use vi
Does pdb2gmx crash in both cases?
If it does, we'll need more information, including what exactly you've done to
each file (i.e. show the contents) because there's an outside chance something
else may be goin
in windows , I use ultraedit, in linux ,use vi
--- 12年6月3日，周日, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] Atomtype 1
收件人: "Discussion list for GROMACS users"
日期: 2012年6月3日,周日,下午9:19
On 6/3/12 9:16 AM, xi zhao wrote:
>
> I use Ultraedit to produce new part and paste
On 6/3/12 9:16 AM, xi zhao wrote:
I use Ultraedit to produce new part and paste the files; we add a residue name
and corresponding atom type and interaction parameters
Having never used a commercial text editor, I don't know if its integrity. What
happens if you use a different editor, li
I use Ultraedit to produce new part and paste the files; we add a residue name
and corresponding atom type and interaction parameters
--- 12年6月3日，周日, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] Atomtype 1
收件人: "Discussion list for GROMACS users"
日期: 2012年6月3日,周日,下午8:46
On 3/06/2012 11:03 PM, xi zhao wrote:
in fact, the pdb2gmx still hang. I modified the atomtypes.atp ,
aminoacids.rtp , ffbonded.itp, ffnonbonded.itp ,
aminoacids.hdb, residuetypes.dat4
,morever, now the pdb2gmx_d even does not the standard protein structure.
So clearly you have broken the file
in fact, the pdb2gmx still hang. I modified the atomtypes.atp ,
aminoacids.rtp , ffbonded.itp, ffnonbonded.itp ,
aminoacids.hdb, residuetypes.dat
,morever, now the pdb2gmx_d even does not the standard protein structure.
--- 12年6月3日，周日, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx
in fact, the program hang.
--- 12年6月3日，周日, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] Atomtype 1
收件人: "Discussion list for GROMACS users"
日期: 2012年6月3日,周日,下午8:46
On 6/3/12 8:24 AM, xi zhao wrote:
> Dear gmx-users:
> I add a new residue in *rtp ,according to
> http
On 6/3/12 8:24 AM, xi zhao wrote:
Dear gmx-users:
I add a new residue in *rtp ,according to
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
and modified corresponding files :such as atp, hdb , after making a full copy of
the installed forcefield in woring diector
Dear gmx-users:
I add a new residue in *rtp ,according to
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
and modified corresponding files :such as atp, hdb , after making a full copy
of the installed forcefield in woring diectory.
When pdb2gmx_d
appeared "
On Sun, 2012-06-03 at 10:47 +0200, Erik Marklund wrote:
> I once took this course in Amsterdam and can highly recommend it:
> http://molsim.chem.uva.nl/molsim2012/index.html
>
Me too. Almost all of the PhD students, who join the group where I am
currently working in, go there and so far everbody
Thanks.
Acoot
From: Erik Marklund
To: Discussion list for GROMACS users
Sent: Sunday, 3 June 2012 7:03 PM
Subject: Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
Hi,
Why don't you do the calculations yourself? You have two HB-energy estimators
and Gromacs at your
Hi,
Why don't you do the calculations yourself? You have two HB-energy estimators
and Gromacs at your disposal.
I myself have not verified this, but colleagues have seen a good match between
the energy obtained from Espinoza's formula and the populations of HA-distances
in simulations.
Best,
I once took this course in Amsterdam and can highly recommend it:
http://molsim.chem.uva.nl/molsim2012/index.html
31 maj 2012 kl. 19.44 skrev edward.de...@gmail.com:
> Dear all,
> does anyone know of any MD or gromacs training course in the coming months?
> All the best
> g-
>
> --
> S
Dear All,
I want to know whether the hydrogen bond energy calculated by the hydrogen bond
energy calculation formula alone is higher than the corresponding energy
calculated by GROMACS only based on the distance of the key atoms and the
charge of the key atoms (of course for hydrogen bond no c
On the same topic, Espinoza et al. also developed a good estimator for HB
energy. See E. Espinosa, E. Molins, C. Lecomte, Chem. Phys. Lett., 285 (1998),
p. 170.
31 maj 2012 kl. 16.51 skrev ABEL Stephane 175950:
> Hi,
>
> Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy
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