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
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
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
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
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