Re: [gmx-users] question about dihedral angle in *.itp file

linfu wrote: > Dear GMX community! > > I have a question about dihedral angle in *.itp file. > question 1: > > why several torsional dihedral angles with different parameters can be defined > on the same set of atoms i, j, k, and l. why not? > > question 2: > > how do we get multiplicity m i

Re: [gmx-users] Error when adding a unnatural amio acid

yuemin liu wrote: Hi, Everyone, I got Error when adding a unnatural amio acid in a protein. I have all the rtp and hdb file modified using information either from ffgmx.rtp ffgmx.hdb or thr rtp file form progdrg. There is no H1 in either rtp file or my new pdb file. When I try use pdb2gmx to gen

[gmx-users] question about dihedral angle in *.itp file

Dear GMX community! I have a question about dihedral angle in *.itp file. question 1: why several torsional dihedral angles with different parameters can be defined on the same set of atoms i, j, k, and l. question 2: how do we get multiplicity m if we want to make some parameter for some tors

RE: [gmx-users] Error when adding a unnatural amio acid

Please check the xlateat.dat file in share/top/ There is one line in it protein HT1H1 which will automatically change your atom name "HT1" to H1. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singap

Re: [gmx-users] Error when adding a unnatural amio acid

You may try add residue name ASO to the end of /top/aminoacids.dat and also increment the number on the top. Regards, Yang Ye On 1/3/2007 8:55 AM, yuemin liu wrote: Hi, Everyone, I got Error when adding a unnatural amio acid in a protein. I have all the rtp and hdb file modified using informa

[gmx-users] Error when adding a unnatural amio acid

Hi, Everyone, I got Error when adding a unnatural amio acid in a protein. I have all the rtp and hdb file modified using information either from ffgmx.rtp ffgmx.hdb or thr rtp file form progdrg. There is no H1 in either rtp file or my new pdb file. When I try use pdb2gmx to generate top file, it a

Re: [gmx-users] problem with g_energy tool

Tere hommikust, Koit Harrievich! Sain Gromacs-st vastust (allpool). Kuna, minu arust, meil on suured fluktuatsioonid (ja need oli ka toodud kirjas), siis ma ei saa aru, mis pärast siin pakutakse niisugune variant. Aga proovisin teha, nagu siin pakutakse. Küsimus oli ainult Ezero valimisest. Sellek

Re: [gmx-users] Benchmarking for Intel Core 2 Extreme QX6700 CPU

Hi, On Jan 2, 2007, at 4:15 PM, Eran Bosis wrote: We are considering purchasing an HP xw4400 workstation with Intel Core 2 Extreme QX6700 CPU. It is a quad-core and we were wondering whether it would be 2x faster than a dual-core Intel Core 2 Duo E6700. Meaning, we intend to run two seperat

[gmx-users] g_chi

Dear GROMACS users, I have some questions about g_chi. For the outputs from -o, -g, -coor, -phi, and -psi, what's the best information one can get from them? In another word, how should one read those output files? Another question: if one wants to see the correlation between the secondary

[gmx-users] Benchmarking for Intel Core 2 Extreme QX6700 CPU

Hi All We are considering purchasing an HP xw4400 workstation with Intel Core 2 Extreme QX6700 CPU. It is a quad-core and we were wondering whether it would be 2x faster than a dual-core Intel Core 2 Duo E6700. Meaning, we intend to run two seperate processes, each one using two cores, would each

Re: [gmx-users] mdrun error during pr

Hi, What's settings for tc-grps, tau_t and ref_t in your mdp files? Regards, Yang Ye On 1/2/2007 8:59 PM, Dhananjay wrote: Hello all, I have minimized the pdb file and wish to do mdrun for position restrain dynamics. For this when I run grompp programm, it is showing error as follows. I do

Re: [gmx-users] Re: Some questions about genbox and EM (Tsjerk Wassenaar)

Hi Zhongqiao Hu, You didn't mention that your system consisted of protein crystals. Maybe I shouldn't have just assumed that it was about proteins in solution, but still... I am running MD simulation in some protein crystals. I always find that the water density in some big pore within protein

Re: [gmx-users] Re: Some questions about genbox and EM (Tsjerk Wassenaar)

2 jan 2007 kl. 15.05 skrev Hu Zhongqiao: Thanks, Tsjerk > >1) Do I need to use genbox to add H2O twice? >> In the past, I first used genbox to add H2O and then used genion to add >> counterion. After that is EM. But now I find, if I use genbox again after >> genion or even after EM, there

[gmx-users] Re: Some questions about genbox and EM (Tsjerk Wassenaar)

Thanks, Tsjerk > >1) Do I need to use genbox to add H2O twice? >> In the past, I first used genbox to add H2O and then used genion to add >> counterion. After that is EM. But now I find, if I use genbox again after >> genion or even after EM, there are some additional, though very few, H2O >> mol

Re: [gmx-users] Some questions about genbox and EM

Hi Zhongqiao Hu, Now I have 3 questions. 1) Do I need to use genbox to add H2O twice? In the past, I first used genbox to add H2O and then used genion to add counterion. After that is EM. But now I find, if I use genbox again after genion or even after EM, there are some additional, though v

Re: [gmx-users] mdrun error during pr

Hi Dhananjay, Happy new year :) Just what it says: not enough ref_t and tau_t values. You use "Protein" and "Sol" as temperature coupling groups, but likely, you also have ions in your system, which are not coupled now. You may want to use "Protein" and "Non-Protein" in stead. In case you have s

[gmx-users] Some questions about genbox and EM

Dear all, Now I have 3 questions. 1) Do I need to use genbox to add H2O twice? In the past, I first used genbox to add H2O and then used genion to add counterion. After that is EM. But now I find, if I use genbox again after genion or even after EM, there are some additional, though very few, H

Re: [gmx-users] ghbond/- hbn option

On Tue, 2007-01-02 at 14:54 +0200, OZGE ENGIN wrote: > Hi, > > I have a problem with the -hbn option. I could not understand the output > given. It is indicated that there is only one type of hydrogen bond is formed > between the donor and acceptor (Only one triplet is given). It means that th

[gmx-users] mdrun error during pr

Hello all, I have minimized the pdb file and wish to do mdrun for position restrain dynamics. For this when I run grompp programm, it is showing error as follows. I don't understand why it is showing this error: processing coordinates... double-checking input for internal consistency... Velociti

[gmx-users] ghbond/- hbn option

Hi, I have a problem with the -hbn option. I could not understand the output given. It is indicated that there is only one type of hydrogen bond is formed between the donor and acceptor (Only one triplet is given). It means that the same hydrogen bond is formed between the same atoms during th