[gmx-users] ffamber99sb error

Dear GROMACS users, I'll be most thankful for any comment/help you might have regarding the following error that I'm encountering in grompp_d : Atomtype amber99_34 not found In ffamber99sb.rtp, amber99_34 refers to the N atom of each amino acid. Thanks a lot Arik -- gmx-users mailing list

Re: [gmx-users] grompp error(Segmentation fault)

other OPLS compatible protein: bpti). I'm still interested in running my program with the amber forcefiled as to be compatible with other calculations being done in the group. I would be most thankful for any suggestion you might have. Thanks a lot Arik On 4/24/2010 5:23 PM, Arik C

Re: [gmx-users] grompp error(Segmentation fault)

ery instance of grompp fail? Do other inputs work? What does "grompp -h" do? 3. Does grompp seg fault with totally different systems (different force fields)? -Justin Arik Cohen wrote: Thank a lot for your very fast response !. Here are the requested details: 1. Version 4.07 is being

Re: [gmx-users] grompp error(Segmentation fault)

Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sbbon.itp Segmentation fault (core dumped) Thanks a lot in advance for all your help Arik On 4/23/2010 4:45 PM, Mark Abraham wrote: On 24/04/2010 7:28 AM, Arik Cohen wrote: I'll be most thankful if any one would be able

[gmx-users] grompp error(Segmentation fault)

I'll be most thankful if any one would be able to help me with the following problem. While running the grompp (in both single and double precision) command I get a Segmentation fault (core dumped) error. The error persist even after recompiling the GROMACS with gcc-4.4.3(previously I was runn

Re: [gmx-users] Amber and protonation state

Thanks a lot for the quick response Arik On 2/26/2010 3:54 AM, Justin A. Lemkul wrote: Arik Cohen wrote: Dear users, I would be most thankful for any comment or advice on the following problems: 1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield. While executin

[gmx-users] Amber and protonation state

Dear users, I would be most thankful for any comment or advice on the following problems: 1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield. While executing the pdb2gmx command as: pdb2gmx -f 1bgq.pdb -water tip3p -his the -his option does not work regardless of the choice

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

Thanks a lot the ultrafast response ! Arik Justin A. Lemkul wrote: Arik Cohen wrote: Dear Gromacs users, In continuation to the problem below, it seems that self interaction is not the problem since a -d 1.5nm around the protein should have been more than enough. Not noticing earlier, I

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

t/suggestion as to how to prevent this drift which causes in turn to the "fragment" problem. Thank Arik Mark James Abraham wrote: On 01/01/10, *"Justin A. Lemkul" * wrote: Arik Cohen wrote: >No, sorry for the confusion. The images are only from a simulation of o

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

thanks Arik Mark James Abraham wrote: On 01/01/10, *"Justin A. Lemkul" * wrote: Arik Cohen wrote: >No, sorry for the confusion. The images are only from a simulation of one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI was a bit different in a way that o

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

Again Thanks a lot Arik Justin A. Lemkul wrote: Arik Cohen wrote: No, sorry for the confusion. The images are only from a simulation of one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI was a bit different in a way that only 1 C-alpha was "detached" (

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

No, sorry for the confusion. The images are only from a simulation of one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI was a bit different in a way that only 1 C-alpha was "detached" (cell size ?). Arik Justin A. Lemkul wrote: Arik Cohen wrote: Which two pr

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

Which two proteins ? I have at least in beginning only one protein which some how is divided into two along the calculation. Any way I'll try both increasing the cell and fix it with trjconv. Thanks a lot Arik Justin A. Lemkul wrote: Arik Cohen wrote: I'm using dodecahedron -d 0

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

I'm using dodecahedron -d 0.7 Justin A. Lemkul wrote: Arik Cohen wrote: Hi, I have not tried yet to fix it with trjconv which I will . Attached is a picture with 4 snapshots taken from the simulation. The C-alphas in question are emphasized with red color. Is your unit

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

ition, the "detached" group includes three segments of the protein(8 residues(126-131), 8 residues(157-164) and 4 residues186-189). Thanks a lot Arik Justin A. Lemkul wrote: Arik Cohen wrote: Hi, With regards to your question I do see some periodicity in which for a section of time in

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

ave in the matter. Thanks Arik Mark Abraham wrote: Arik Cohen wrote: Hi, Thanks for answering so quickly !. Apparently whole residues have detached from the protein. So... like I asked last time, are you seeing a periodicity artefact? "Detached" covers a whole gamut of possibilitie

[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

part. Thanks allot for all your help Arik Mark Abraham wrote: Arik Cohen wrote: Dear GROMACS users, While running a simple MD simulation with both a small protein such as BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm encountering an odd situation in which one (in the ca

[gmx-users] A problem with a "detaching Calpha/s"

Dear GROMACS users, While running a simple MD simulation with both a small protein such as BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm encountering an odd situation in which one (in the case of BPTI) or several Calphas (in the later case) are "detaching them selfs" from the m

Re: [gmx-users] g_energy

Thanks allot for the ultrafast response and above all your help !. Arik Mark Abraham wrote: Arik Cohen wrote: Hi, Is there a way to tell the g_energy program the output option(i.e. Potential, Temperature ) in advance when you run the program. Namely, I would like to know if there is a

[gmx-users] g_energy

Hi, Is there a way to tell the g_energy program the output option(i.e. Potential, Temperature ) in advance when you run the program. Namely, I would like to know if there is a flag that I can give the program and thus skip the part when the g_energy program asks for an input for the Pote

Re: [gmx-users] Extended trajectory

Thanks allot for all your help Arik Justin A. Lemkul wrote: Arik Cohen wrote: Hi, I'll be most thankful if someone could tell me how to run a fragmented trajectory using only the mdrun command. As of now I'm using : while(SimuTime < SimTime) { ... syste

[gmx-users] Extended trajectory

Hi, I'll be most thankful if someone could tell me how to run a fragmented trajectory using only the mdrun command. As of now I'm using : while(SimuTime < SimTime) { ... system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o run.tpr"); system("mdrun -cpi run.cpt -cpo

[gmx-users] A fragmented trajectory

Dear users, I'll be most thankful if someone could give me an example as how to restart a MD simulation that is been fragmented into several sections. I have tried several flags according to the manual with no success. Every time a different problem emerges, i.e. either the simulation get stuc

Re: [gmx-users] Snapshots in different files

users-boun...@gromacs.org] *On Behalf Of *Arik Cohen *Sent:* Thursday, 8 October 2009 9:27 AM *To:* Discussion list for GROMACS users *Subject:* Re: [gmx-users] Snapshots in different files Thanks for answering. This would not be the case so much since another program(sniffer) can be working along si

Re: [gmx-users] Snapshots in different files

e the snapshot. The aim here is to do an MD from which an ensemble of the C-alpha will be created. Thanks again Arik Mark Abraham wrote: Arik Cohen wrote: Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a

Re: [gmx-users] Snapshots in different files

Thanks allot for all your help and ultrafast response. Arik Justin A. Lemkul wrote: Arik Cohen wrote: Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a different file on the fly. Not possible, as far a

Re: [gmx-users] Snapshots in different files

Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a different file on the fly. Thanks Arik Justin A. Lemkul wrote: Arik Cohen wrote: Dear users, Is there a way to take a snapshot along the trajectory and

[gmx-users] Snapshots in different files

Dear users, Is there a way to take a snapshot along the trajectory and write it into a different file, so that each snapshot will be written into its own file named with its own index ?(e.g. snap_1, snap_2 ) Thanks Arik ___ gmx-users mailing li

Re: [gmx-users] Snapshot taken under certain condition

Thanks allot for all your help Arik Mark Abraham wrote: Arik Cohen wrote: Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? If you know in advance

Re: [gmx-users] Snapshot taken under certain condition

Thanks for all your help and rapid response. Arik Justin A. Lemkul wrote: Arik Cohen wrote: Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? No

[gmx-users] Snapshot taken under certain condition

Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? Thanks Arik ___ gmx-users mailing listgmx-users@gromacs.o