Hi
In John's GROMACS tutorial for solvation study of spider toxin peptide, he
has
included a suggested em.mdp files to set up an in vacuo minimization.
But I had some noted while conducting the grompp before em.
Analysing residue names:
There are:35Protein residues
Analysing Protein...
Kavyashree M wrote:
Sir,
System is a protein with 123 aa. No modifications were made on the
pdb file,
and it was submitted to pdb2gmx by removing all HETATMs, retaining only
protein
atoms. topology was created entirely by pdb2gmx and no other molecule
was introduced.
I will go
Dear Justin
I read your articles about PRODRG server,they were very useful.
But I have a question:
are charges of functional groups and generally other atom groups the same in
all force fields?
Because you have modified charges of your molecules by Gromos96 53A6 while
prodrg server is generating
Sir,
Yes sir I am using PME. And one more thing I noticed was, the protein
has
7 disulphide bonds, so when I reduce all the cystine to cysteine or to
alanine,
the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and also
the
value of this is identical in case of alanine
Kavyashree M wrote:
Sir,
Yes sir I am using PME. And one more thing I noticed was, the
protein has
7 disulphide bonds, so when I reduce all the cystine to cysteine or to
alanine,
the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and
also the
value of this is
mohsen ramezanpour wrote:
Dear Justin
I read your articles about PRODRG server,they were very useful.
But I have a question:
are charges of functional groups and generally other atom groups the
same in all force fields?
Because you have modified charges of your molecules by Gromos96 53A6
Ok
then,I can use PRODRG server to generate .top and .gro files for drug.
since it's reported charges are not very accurate ,we can replace all
charges completely with them in 53A6(if was present).
But it means we are working in 53A6 force field.
then,we must generate .top and .gro files for our
Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham:
On 21/01/2011 6:47 AM, Christian Mötzing wrote:
Hi,
I currently read through the GMX manual 4.5.3. I have two questions:
1) Density is calculated by the density of the material and the box
volume. But I can't find a
mohsen ramezanpour wrote:
Ok
then,I can use PRODRG server to generate .top and .gro files for drug.
since it's reported charges are not very accurate ,we can replace all
charges completely with them in 53A6(if was present).
But it means we are working in 53A6 force field.
then,we must
I went through few papers related to OPLS-AA, but could not find
any specific values mentioned for vdw and coulomb intecations..
In one of the papers
.In most cases, the intermolecular nonbonded interactions were
truncated at 11Å based on roughly the center-of-mass separations
with quadratic
Kavyashree M wrote:
I went through few papers related to OPLS-AA, but could not find
any specific values mentioned for vdw and coulomb intecations..
In one of the papers
.In most cases, the intermolecular nonbonded interactions were
truncated at 11Å based on roughly the center-of-mass
Dear Justin,
I manually specify termini. I choosed None but I have the same error.
Fatal error:
atom C not found in residue 13NH2 while combining tdb and rtp
22 Ocak 2011 00:45 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı:
ahmet yıldırım wrote:
Dear justin,
I looked at the pdb
ahmet yıldırım wrote:
Dear Justin,
I manually specify termini. I choosed None but I have the same error.
Fatal error:
atom C not found in residue 13NH2 while combining tdb and rtp
Please post your .pdb file.
-Justin
22 Ocak 2011 00:45 tarihinde Justin A. Lemkul jalem...@vt.edu
ahmet yıldırım wrote:
please look at the attached file
I had no problem making a topology.
$ pdb2gmx -f 3MOA.pdb -ter
...
Using the Gromos43a1 force field in directory gromos43a1.ff
...
Select start terminus type for GLU-659
0: NH3+
1: NH2
2: None
0
Start terminus GLU-659: NH3+
Select
Thank you very much
22 Ocak 2011 23:07 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı:
ahmet yıldırım wrote:
please look at the attached file
I had no problem making a topology.
$ pdb2gmx -f 3MOA.pdb -ter
...
Using the Gromos43a1 force field in directory gromos43a1.ff
...
Select
Dear Justin,
Fatal Error:
Chain identifier 'A' was used in two non-sequential blocks (residue 710,
atom 5449)
I have sometimes this error for some pdb files.
1. Missing atom and residues entries, that GROMACS is unable to reconstruct.
2. HETATM entries which can not be processed using pdb2gmx.
ahmet yıldırım wrote:
Dear Justin,
Fatal Error:
Chain identifier 'A' was used in two non-sequential blocks (residue 710,
atom 5449)
I have sometimes this error for some pdb files.
1. Missing atom and residues entries, that GROMACS is unable to reconstruct.
2. HETATM entries which can not be
On 23/01/2011 2:36 AM, Christian Mötzing wrote:
Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham:
On 21/01/2011 6:47 AM, Christian Mötzing wrote:
Hi,
I currently read through the GMX manual 4.5.3. I have two questions:
1) Density is calculated by the density of the material and
Dear all,
This must be a pretty simple problem but I am stuck nonetheless. I have been
using the lipids from Prof Tieleman's website without any problem on gromacs
4.0.7.
Now that I've got 4.5.3 installed, I want to try the g_membed tool but have
encountered these problems.
Following
Oops sorry!
I found the mistake...
the topology file should read
gromos53a6_lipid.ff/forcefield.itp instead of gromos53a6.ff/forcefield.itp
silly me
From: gmx-users-boun...@gromacs.org on behalf of NG HUI WEN
Sent: Sun 1/23/2011 1:40 PM
To:
Dear gromacs users,
I went through the papers dx.doi.org/10.1021/jp003919d. on OPLS,
Its is stated in the paper
Intermolecular interactions were truncated at 11 Å, with the standard
correction for the interactions beyond that radius. The electrostatic
interactions were quadratically feathered
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