Re: [gmx-users] PRODRG server issues

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

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 charges

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

Re: [gmx-users] PRODRG charges

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

Re: [gmx-users] PRODRG charges

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

Re: [gmx-users] PRODRG charges

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

[gmx-users] PRODRG charges

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

Re: [gmx-users] PRODRG server

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

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 topology

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

[gmx-users] PRODRG topology

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

Re: [gmx-users] PRODRG tools

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

Re: [gmx-users] PRODRG tools

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. -

[gmx-users] PRODRG tools

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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

[gmx-users] PRODRG

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.

Re: [gmx-users] PRODRG server

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

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

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

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

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

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

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

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

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

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

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

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

Re: [gmx-users] PRODRG crash

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

[gmx-users] PRODRG crash

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

Re: [gmx-users] PRODRG

, 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

: 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

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 misconception about how to use Gromacs. Specifically, t

Re: [gmx-users] PRODRG

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

Re: [gmx-users] PRODRG

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,

[gmx-users] PRODRG

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

Re: [gmx-users] prodrg 4.5beta generated topologies and exclusions

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

[gmx-users] prodrg 4.5beta generated topologies and exclusions

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

Re: [gmx-users] prodrg

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

[gmx-users] prodrg

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

[gmx-users] prodrg compilation

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

Re: [gmx-users] prodrg and charge groups

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

[gmx-users] prodrg and charge groups

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