Re: [gmx-users] PRODRG server issues

2012-05-22 Thread Justin A. Lemkul
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

[gmx-users] PRODRG server issues

2012-05-22 Thread rainy908
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

Re: [gmx-users] PRODRG server

2011-11-18 Thread Justin A. Lemkul
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

[gmx-users] PRODRG server

2011-11-18 Thread swati patel
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

Re: [gmx-users] PRODRG server

2011-01-24 Thread Justin A. Lemkul
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

Re: [gmx-users] PRODRG server

2011-01-24 Thread mohsen ramezanpour
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

Re: [gmx-users] PRODRG server

2011-01-24 Thread Justin A. Lemkul
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'

Re: [gmx-users] PRODRG server

2011-01-24 Thread Mark Abraham
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

Re: [gmx-users] PRODRG server

2011-01-24 Thread mohsen ramezanpour
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

Re: [gmx-users] PRODRG server

2011-01-22 Thread Justin A. Lemkul
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

Re: [gmx-users] PRODRG server

2011-01-22 Thread mohsen ramezanpour
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

Re: [gmx-users] PRODRG server

2011-01-22 Thread Justin A. Lemkul
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

[gmx-users] PRODRG server

2011-01-22 Thread mohsen ramezanpour
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

Re: [gmx-users] PRODRG server

2011-01-19 Thread Justin A. Lemkul
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

[gmx-users] PRODRG server

2011-01-19 Thread mohsen ramezanpour
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

[gmx-users] PRODRG server

2010-10-16 Thread mohsen ramezanpour
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