On 5/22/12 8:49 PM, rainy908 wrote:
All:
I know this question isn't particularly related to GROMACS, but I've contacted
the PRODRG admin in the past have never received a response. That said, is
anyone experiencing technical issues acquiring a token to use PRODRG after
entering an email ad
All:
I know this question isn't particularly related to GROMACS, but I've contacted
the PRODRG admin in the past have never received a response. That said, is
anyone experiencing technical issues acquiring a token to use PRODRG after
entering an email address?
http://davapc1.bioch.dundee.ac.u
On 12/01/2012 10:42 PM, g...@bioacademy.gr wrote:
Hi
Many thanks for your reply and sorry to come back on this.
Is the fitting to experimental free energies of solvation, the
only acceptable way to get "GROMOS-compatible charges"? Acceptable
because this is the way that partial charges were der
On 2012-01-12 12:42, g...@bioacademy.gr wrote:
Hi
Many thanks for your reply and sorry to come back on this.
Is the fitting to experimental free energies of solvation, the
only acceptable way to get "GROMOS-compatible charges"? Acceptable
because this is the way that partial charges were derive
Hi
Many thanks for your reply and sorry to come back on this.
Is the fitting to experimental free energies of solvation, the
only acceptable way to get "GROMOS-compatible charges"? Acceptable
because this is the way that partial charges were derived for the
gromos ff.
In the quite usual case tha
g...@bioacademy.gr wrote:
Hello
Given that the partial charges from PRODRG are not reliable (as explained
Justin Lemkul's paper),
are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable
starting point?
Yes, those charges are a reasonable start, but will almost certainly not
Hello
Given that the partial charges from PRODRG are not reliable (as explained
Justin Lemkul's paper),
are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable
starting point?
In this case, do we treat all ligand atoms as one charge group?
Thanks.
George
--
gmx-users mailing
swati patel wrote:
Hello Justin,
Sorry for again and again bothering you.But in prodrg2.5 server,there is
no option to choose force fields.It automatically generates topology in
gromos 87 force fields.
The default force field used by the latest PRODRG is Gromos96 43a1, not
Gromos87.
-J
Hello Justin,
Sorry for again and again bothering you.But in prodrg2.5 server,there is no
option to choose force fields.It automatically generates topology in gromos
87 force fields.
I am using 4.5 version of gromacs in which gromos force fields are gromos
96.How to match my protein and ligand to
Marzinek, Jan wrote:
Dear Gromacs Users,
I used PRODRG server in order to obtain the topology file for my
molecule (52 atoms with all hydrogens). However, server generated
Gromacs topology which involves 47 atoms (for PDB file with
polar/aromatic hydrogens). Whether I will use the pdb fi
Dear Gromacs Users,
I used PRODRG server in order to obtain the topology file for my molecule (52
atoms with all hydrogens). However, server generated Gromacs topology which
involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will
use the pdb file with missing 4 hydrogen
Actually, you can use other parametrization tools like antechamber (for
amber) or cgenff (for charmm).
>
>
> Liu Shiyong wrote:
>> Dear all,
>>
>>Is there any other free tool like PRODRG ? PRODRG server couldn't
>> read PDB file from user any more. It 's not easy to get a free version
>> asap
Liu Shiyong wrote:
Dear all,
Is there any other free tool like PRODRG ? PRODRG server couldn't
read PDB file from user any more. It 's not easy to get a free version asap.
You can contact the maintainers for a standalone version of PRODRG. Then you
can run it whenever you want.
-
Dear all,
Is there any other free tool like PRODRG ? PRODRG server couldn't read
PDB file from user any more. It 's not easy to get a free version asap.
Best
Shiyong
--
Shiyong Liu
--
Biomolecular Physics and Modeling Gro
On 11/02/2011 8:18 PM, mohsen ramezanpour wrote:
Dear Dr.Justin
I did it,it works.Thanks.
there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
As Justin suggest
mohsen ramezanpour wrote:
Dear Dr.Justin
I did it,it works.Thanks.
there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
Use a different force field and don't
Dear Dr.Justin
I did it,it works.Thanks.
there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
Thanks in advance
Mohsen
On Thu, Feb 10, 2011 at 7:56 PM, Justin A. L
mohsen ramezanpour wrote:
Dear Dr.Justin
I have read this section before.
There are 2 problem:
1:ADDHYD atomname and DELHYD atomname commands dosen't work!
they result in ERROR in PRODRG
You have to run PRODRG twice. The first time, you get the wrong output. Note
the atom name that PROD
Dear Dr.Justin
I have read this section before.
There are 2 problem:
1:ADDHYD atomname and DELHYD atomname commands dosen't work!
they result in ERROR in PRODRG
2:Actually I don't know the additional hydrogen is necessary or not!
Because it may be necessary for proper protonation.
My drug(Sertra
I'm completely in agreement with that advice. To use antechamber tool, I
recommend use force field for all the system.
>
> The OP's question is easily answered by referring to the PRODRG FAQ in
> dealing
> with proper protonation.
>
> As for Antechamber and the like, these are good tools, but do
The OP's question is easily answered by referring to the PRODRG FAQ in dealing
with proper protonation.
As for Antechamber and the like, these are good tools, but do not produce
GROMOS-compatible topologies, if that is indeed the underlying goal. We've done
thorough analysis of various QM c
Yes I would recommend acpype.
On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote:
> I think that is better to use antechamber tools.
>
>
> > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
> >> Dear Users
I think that is better to use antechamber tools.
> On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>> Dear Users
>>
>> I am using PRODRG to make topology for my drug
>> It addes Hydrogenes but in wrong way.
>> My Nitrogen atom is bonded to 2 Carbos,
>> and PRODRG addes 2 Hydrogenes to it .
>> Pl
On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
Dear Users
I am using PRODRG to make topology for my drug
It addes Hydrogenes but in wrong way.
My Nitrogen atom is bonded to 2 Carbos,
and PRODRG addes 2 Hydrogenes to it .
Please let me know how can I do.
Thanks in advance
This is not really t
Dear Users
I am using PRODRG to make topology for my drug
It addes Hydrogenes but in wrong way.
My Nitrogen atom is bonded to 2 Carbos,
and PRODRG addes 2 Hydrogenes to it .
Please let me know how can I do.
Thanks in advance
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.
mohsen ramezanpour wrote:
Thanks for your guidance.
I looked that file,But I think the name of functional groups are
different in .rtp file because I can't find no one of them in this file.
Functional group names are not in the .rtp files. You locate applicable
functional groups by knowi
Thanks for your guidance.
I looked that file,But I think the name of functional groups are different
in .rtp file because I can't find no one of them in this file.
please let me know how can I know the correct name f or functional groups
for example:HYDROXYL,CARBOXYL,HALO,AMINO and ...
Thanks in
mohsen ramezanpour wrote:
Dear Dr.justin
Actually by doing this we are using two different force fields in one
simulation.
I had done it before and the result was that I discussed before in
gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)
Then,this approch seems to doesn'
On 24/01/2011 10:06 PM, mohsen ramezanpour wrote:
Dear Dr.justin
Actually by doing this we are using two different force fields in one
simulation.
I had done it before and the result was that I discussed before in
gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)
Then,this a
Dear Dr.justin
Actually by doing this we are using two different force fields in one
simulation.
I had done it before and the result was that I discussed before in
gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)
Then,this approch seems to doesn't work about my system.
Then I
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 genera
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 p
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
whi
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 t
mohsen ramezanpour wrote:
Dear All
I generated toplogy file for a drug by PRODG server.
How can I validate it?
i looked at these links but there are not a way for doing that.
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Downloads/Related_Software/PRODRG#T
Dear All
I generated toplogy file for a drug by PRODG server.
How can I validate it?
i looked at these links but there are not a way for doing that.
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
thanks in advance
--
gmx
Dear gromacs users
I have a pdb file who include protein and a drug.I separated them by pymol
software and saved them separately.now I want to make topology and gro file
for it but
I am facing with this page below.can you guid me?
thanks in advance.
PRODRG> Starting up PRODRG version 071121.0636
Moeed wrote:
Dear Justin,
Actually, I used -d option because you said the atoms in the box must be
half a bond length from the edges of box...I thought maybe this can be
done by -d...
My point was that you should not be using a combination of -box, -d, and -angles
simultaneously. Use e
Dear Justin,
Actually, I used -d option because you said the atoms in the box must be
half a bond length from the edges of box...I thought maybe this can be done
by -d...
With PRODRG I am unable to produce coordinate file a chain with less than
three C atoms.
I sketched the molecules:
C-C ethane
, followed by energy
minimization.
-Justin
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Wed 10/7/2009 1:11 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PRODRG
jorge_quint...@ciencias.uis.edu.co wrote:
Hello Chanel
: Re: [gmx-users] PRODRG
jorge_quint...@ciencias.uis.edu.co wrote:
> Hello Chanel
>
> Could you send a copy of the PDB file. I think that the error is related
> with label atoms included in each force fiel parameter.
>
More likely this is yet another case of a common misconce
jorge_quint...@ciencias.uis.edu.co wrote:
Hello Chanel
Could you send a copy of the PDB file. I think that the error is related
with label atoms included in each force fiel parameter.
More likely this is yet another case of a common misconception about how to use
Gromacs. Specifically, t
Hello Chanel
Could you send a copy of the PDB file. I think that the error is related
with label atoms included in each force fiel parameter.
See you.
> Hello,
> I have recently made a pdb file using the Dundee PRODRG server.
> However, when I try to use this pdb in gromacs, I receive an e
Smith, Chanel Chonda wrote:
Hello,
I have recently made a pdb file using the Dundee PRODRG server.
However, when I try to use this pdb in gromacs, I receive an error message
that states: "DRG is not in the topology database." I have tried to use the
available tutorial to solve this issue,
Hello,
I have recently made a pdb file using the Dundee PRODRG server.
However, when I try to use this pdb in gromacs, I receive an error message
that states: "DRG is not in the topology database." I have tried to use the
available tutorial to solve this issue, but with not much success. Cou
Dean Cue bas wrote:
Hello all. Just a quick clarification, please.
Reading the original GROMOS53A6 paper, it appears that 2nd neighbor
(1-3) interactions are always excluded, and that third neighbor (1-4)
non-bonding interactions are used, yet modified in some circumstances.
The paper also st
Hello all. Just a quick clarification, please.
Reading the original GROMOS53A6 paper, it appears that 2nd neighbor (1-3)
interactions are always excluded, and that third neighbor (1-4) non-bonding
interactions are used, yet modified in some circumstances. The paper also
states that all (1-4) inter
Bhawana Gupta wrote:
hello everyone,
Pls tell me whether we can use PRODRG server only for generating
peptides with unusual amino acid through JME or it can be used for the
peptides having usual amino acid.
PRODRG is most useful in obtaining topologies for small molecules. You might
use
hello everyone,
Pls tell me whether we can use PRODRG server only for generating peptides
with unusual amino acid through JME or it can be used for the peptides
having usual amino acid.
whether it is necessary to use pdb2gmx for peptide containing usual amino
acid or we can do it with PRODRG serve
I hvae made a topogy file from prodrg. I have successfully completed before for
many molecules, like ligand of Glucose oxidase. Now when i run grommp
grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em
i get the following error
Program grompp, VERSION 3.3.1
Source code file: topio.c, line: 388
F
Diane,
I can't speak to charge groups, but in terms of charges, I think I
remember that prodrg has a number of disclaimers about its charges.
Personally, I would be rather reluctant to use prodrg charges for
simulating ligands. A fast alternative would be to download the
Antechamber package, whic
Title: prodrg and charge groups
I don't know if this has already been discussed, but I'm wondering how the charges and charge groups are assigned by PRODRG. I'm curious about this because I have been using it for a few similar ligands which all contain a steroid (estradiol) moiety. In the thr
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