[gmx-users] Error in PDB2GMX

ERROR something like this. FATAL ERROR : Incomplete Ring in HIS 69. Now, I am really confused that what will be the solution of this thing. I am also new to GROMACS and I have no idea about the solution of this problem. I would highly appreciate your help for the same. Thanks, Sunny Mishra

[gmx-users] Error in PDB2GMX

Hi Justin, Thanks for the expedient reply. I referred MARTINI but after converting 1A8G.pdb to 1A8G_CG.pdb i.e. CG structure of protein I dnt know how to make the topol.top and conf.gro files for that and also I am not able to generate the posre.itp file with this CG structure because it says the

[gmx-users] Error in PDB2GMX

Thats great. I am able to make now my 1A8G.itp file and also the CG structure of protein but now the other problem which is arising is to make the topol.top file and conf.gro file. When I am making this using the command...pdb2gmx -v -f 1A8G_CG.pdb -o conf.gro -p topol.top ..it says choose the

[gmx-users] water.pdb file

Hi all, Thanks for all the previous help. I am starting to run my protein simulations after going through the MARTINI tutorial. In MARTINI tutorials I was provided with some of the input files but they have also taught that how to make your own input files when you run your own protein simulation.

[gmx-users] water.pdb file

Hi Justin, Thanks for the expedient reply. In the MARTINI tutorial they have provided two water.gro files one for lipids and the other for proteins. Protein water molecule file consists of 10800 atoms of water and the lipid has 400 atoms. So even if I simulate any protein structure after convertin

Re: [gmx-users] water.pdb file

n't know how to create 1K4C.ssd file now because when I try to create it using do_dssp it asks me to generate the topol.tpr file and I cannot generate that before simulation. Do you have any idea about this? Sunny On Mon, Aug 10, 2009 at 6:31 PM, Justin A. Lemkul wrote: > > > s

[gmx-users] dssp output of CG structure of 1K4C

Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C prote

Re: [gmx-users] dssp output of CG structure of 1K4C

, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Dear all, >> >> I wanted to get the dssp output of Coarse Grained structure of my protein >> i.e. 1K4C. In order to get that I have a script which is given to me in the >> M

Re: [gmx-users] dssp output of CG structure of 1K4C

OK. Thanks a lot justin On Tue, Aug 18, 2009 at 1:16 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Hi Justin, >> >> Thanks for the expedient reply. So in that case I cannot get the dssp >> output of my CG structure for sure. So in that case do I

[gmx-users] Re: dssp output of CG structure of 1K4C

Hi Johny and Justin, Thanks for the reply. But another problem here arises regarding the 1K4C_clean.top file. I have to minimize the system in vacuum i.e. without adding any water molecules in it. After making the .gro file from 1K4C_clean.pdb file with the help of genbox command and when I do the

[gmx-users] .top file from .gro file

Hi all, Is there anyway I can generate the .gro file from .top file without using the command pdb2gmx and editconf? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:/

Re: [gmx-users] .top file from .gro file

mulation in vacuum I cannot add anything else. Don't know how to proceed. Thanks, Sunny On Tue, Aug 18, 2009 at 7:00 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Hi all, >> >> Is there anyway I can generate the .gro file from .top file without u

Re: [gmx-users] .top file from .gro file

gram grompp, VERSION 4.0.5 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (1K4C.gro, 4534) does not match topology (1K4C.top, 1166) On Tue, Aug 18, 2009 at 7:24 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >>

Re: [gmx-users] .top file from .gro file

top -maxwarn 10 AM I CORRECT? Sunny On Tue, Aug 18, 2009 at 7:44 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Hi Justin, >> >> I am using these commands... >> >> genbox -cp 1K4C.pdb -box 10 10 10 -o 1K4C.gro >> >> from here I

Re: [gmx-users] .top file from .gro file

gro, 1127) does not match topology (1K4C.top, 1166) ------- On Tue, Aug 18, 2009 at 7:54 PM, sunny mishra wrote: > > Alright sounds good to me. In order to make it sure once againI have to > do something like this... > awk -f atom2cg.awk 1K4

Re: [gmx-users] .top file from .gro file

Ok..I will see that and let you know. Thanks for the help though. Sunny On Tue, Aug 18, 2009 at 8:12 PM, Mark Abraham wrote: > sunny mishra wrote: > >> I did the same but again i get the same error..something like this >> >> awk -f atom2cg_v2.1tryout.awk 1K4C.pdb &

Re: [gmx-users] .top file from .gro file

Hi, I checked both the files they match exactly but still I get the same error message that .gro file and .top file dnt match. I dnt know how to proceed now. Sunny On Tue, Aug 18, 2009 at 8:18 PM, sunny mishra wrote: > Ok..I will see that and let you know. Thanks for the help though. >

Re: [gmx-users] .top file from .gro file

coordinates in coordinate file (1K4C_cleanCG.pdb, 209) does not match topology (1K4C_clean.top, 216) --- I don't know where I have done the mistake...your help will be highly appreciable in this case. Thanks a lot, Sunny On W

Re: [gmx-users] .top file from .gro file

n > of an ARG residue, you can bet this will be a problem. > > -Justin > > > Mark Abraham wrote: > >> sunny mishra wrote: >> >>> Hi Justin, >>> >>> Thanks for the reply and here is the following which I am doing. I would >>> appreciat

Re: [gmx-users] .top file from .gro file

Alright. Sounds good to me. let me check that out and i will let you know the progress. Thanks, Sunny On Wed, Aug 19, 2009 at 7:19 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Hi Mark and Justin, >> >> Thanks for the valuable advise and I want to

Re: [gmx-users] .top file from .gro file

I have to add them then how? for example in my .itp file there are 2 ILE but in my .gro file there is only 1 ILE. So should i add another ILE in my .gro file or delete 2 ILE from .itp and 1ILE from .gro. Thanks in advance. Sunny On Wed, Aug 19, 2009 at 7:23 PM, sunny mishra wrote: > > A

Re: [gmx-users] .top file from .gro file

t him. Can you help me out with this that how to model the original PDB file (1K4C) before I proceed. Thanks, Sunny On Wed, Aug 19, 2009 at 8:25 PM, Mark Abraham wrote: > sunny mishra wrote: > >> Hi Mark and Justin, >> Thanks for the valuable advise and I want to do the

[gmx-users] error in ATOM2CG.awk script

Dear all, I was earlier facing problem regarding the mismatch of atoms in .top and .gro file and then after useful discussion here I figured out that some atoms were missing in my cg.pdb file and that problem is because of the OLDER atom2cg.awk script which MARTINI folks have in their website. When

Re: [gmx-users] error in ATOM2CG.awk script

Yeah I agree wiht you but I tested another protein as well 1BL8 to check if there was a problem specifically in 1K4C. Even after testing 1BL8 it gives me the same error. What do you think? On Thu, Aug 27, 2009 at 4:11 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >>

[gmx-users] mdrun segmentation fault

Dear all, At the final step of my mdrun I get LINCS warning. I don't know whats the issue. Please help me out. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 51.050964, max 314.598846 (between atoms 3 and 4) bonds that rotated more than 30 degrees: atom 1 atom

[gmx-users] g77 error in martini

Dear all, In the martini tutorial there is a approach of martini + ElneDYN . In the tutorial they provided me a script which converts the cleaned pdb structure to CG structure of protein. I compiled the script using g77 (as they recommended) and then I am trying to make the CG structure of 1BL8 pro

[gmx-users] Missing Residues

Hi All, My protein has lots of missing residues and in every chain there are 4-5 missing residues with atom name. I can see missing residues with the help of Swiss PDB Viewer after I load the pdb file. I am very new in Swiss PDB viewer and I would highly appreciate if anyone can let me know how to

[gmx-users] LINCS dependence

Hi, I have a quick question. My system exploded when I tried to run the simulation and it gives me the LINCS warning. I am using MARTINI forcefield and finally I get segmentation fault. I don't know that what are the factors do i need to change to get rid of the LINCS warning. Please let me know. I

Re: [gmx-users] LINCS dependence

= lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 On Tue, Sep 29, 2009 at 4:17 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Hi, >> >> I ha

[gmx-users] Inserting protein in Bilayer

Hi All, I am working on the CG simulations of the proteins and lipid bilayers. I am confused of how to set up the whole system for simulations. I got the DSPC lipid bilayer from martini website and I have 1SU4.pdb file with me. I cleaned the .pdb file and now I want to include the 14 DSPC molecule

Re: [gmx-users] Inserting protein in Bilayer

DSPC molecules. Where should I include them I mean at which step? When I make my .top file for the protein do I include DSPC molecules there or anywhere else? Please let me know Sunny On Sun, Oct 11, 2009 at 4:30 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: >> >> Hi

Re: [gmx-users] Inserting protein in Bilayer

Hi Justin, I have set up the whole system correctly but now at the final step when I do mdrun it gives me the fatal error by saying that Number of grid cells is zero. Probably the system and box collapsed. Do you have any idea about this? Sunny On Sun, Oct 11, 2009 at 4:45 PM, sunny mishra

Re: [gmx-users] Inserting protein in Bilayer

water molecules or lipid with protein as per my interest. I hope you got my question. Thanks for all the previous help and your reply for the same would be highly appreciable Thanks, Sunny On Sun, Oct 11, 2009 at 5:50 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: >> >> H

[gmx-users] Protein Orientation

Dear All, I am following the tutorial given by justin and have question regarding the orientation of protein. Tutorial says that orient the protein along z axis using editconf -princ command followed by the rotation along y axis. My question is that when I use the editconf -princ command, does it

Re: [gmx-users] Protein Orientation

, 2009 at 10:18 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: >> >> Dear All, >> >> I am following the tutorial given by justin and have question >> regarding the orientation of protein. Tutorial says that orient the >> protein along z axis

Re: [gmx-users] Protein Orientation

sure. thanks On Sun, Oct 18, 2009 at 10:45 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: >> >> oh cool. I have gromacs version 4.4 so my protein will be on the x >> axis by default and to orient the long axis of protein along z axis >> then I have to edit

Re: [gmx-users] scripts to generate topology CG

There is a seq2itp.pl script provided by martini folks in their website. You can get it from there. Sunny On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra wrote: > Hi: > I am looking for scripts that generate topology in coarse grained. > Thanks for indications. > > francesco pietra > _

Re: [gmx-users] Aligning protein in bilayer with editconf

Put your protein file in TMDET and it will align the protein for you perpendicular to Z axis and also the protein will be at origin in that case then you can use geom_center script provided in VMD to put the lipid in the origin and move it towards the protein. Hope it helps On Tue, Oct 27, 2009 at

[gmx-users] Inflategro for Coarse Grained

Hi all, After inserting the protein into the lipid bilayer I am working on inflategro script and trying to scale the lipid and do energy minimization. Since I am doing everything in CG so I dnt know whether inflategro is defined for CG or not? Besides that when I run the script provided in http://

[gmx-users] Re: Inflategro for Coarse Grained

tion. What should I do in this case? Sunny On Thu, Oct 29, 2009 at 1:51 PM, sunny mishra wrote: > Dear Thomas, > > I have used the new script as well but that doesn't work either and gives > me the same error. What changes do you think I have to make. If you want I > can se

Re: [gmx-users] Re: Inflategro for Coarse Grained

and protein shud have remained in the center of the lipid but that doesn't happen. I hope you got my question On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Yes I did the same and when I see my system.gro file it gives me the >&g

Re: [gmx-users] Re: Inflategro for Coarse Grained

No. But in order to do that with lipid.gro what co-ordinates should I have to take? On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> okk...here are the commands which I am givng... >> >> editconf -f 1SU4_cleancg_trans.

Re: [gmx-users] Re: Inflategro for Coarse Grained

. Lemkul wrote: > > > sunny mishra wrote: > >> No. But in order to do that with lipid.gro what co-ordinates should I have >> to take? >> >> > I think you need to differentiate between "coordinates" and "box vectors." > You should center

Re: [gmx-users] Re: Inflategro for Coarse Grained

t still at the center so I dnt know whether this will matter a lot or not? On Thu, Oct 29, 2009 at 5:26 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Alright. I have done thisI have made another lipid_newbox.gro file and >> wrote same box vectors as

Re: [gmx-users] Re: Inflategro for Coarse Grained

am trying to ask? Can I do that? On Thu, Oct 29, 2009 at 5:46 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Well yes I guess I am getting the same thing what I expected but now I am >> little confused here and I don't know how to explain you this b

[gmx-users] EM with inflategro

Hi All, I am having a trouble during EM step after I inflategro my lipid.gro (protein is already centered). After doing this : Reading. Scaling lipids There are 512 lipids... with 14 atoms per lipid.. Determining upper and lower leaflet... 240 lipids in the upper... 272 lipids in th

Re: [gmx-users] EM with inflategro

4:49 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Hi All, >> >> I am having a trouble during EM step after I inflategro my lipid.gro >> (protein is already centered). >> >> After doing this : >> >> Reading. >>

[gmx-users] DPPC to CG DPPC

Dear All, I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script wo

Re: [gmx-users] DPPC to CG DPPC

Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any

Re: [gmx-users] DPPC to CG DPPC

Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole wrote: > > No need of position restrained simulation with the CG lipids. > CG is very forgiving :)) > > For proteins it is more delicate. > > On Dec 15, 2009, at 6:02 P

Re: [gmx-users] DPPC to CG DPPC

be soft on the start. PR is one way to do it and you can do similar > to when doing on a atomistic simulation. > > On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: > > Alright thanks. So should I do it for proteins? > > On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole wrote: >

[gmx-users] PR for CG lipid and CG protein

Hi All, I am trying to insert coarse grained protein to coarse grained lipid. My protein is CG 1SU4 and lipid is CG DPPC. I can make a big hole and pack lipids around the protein using INFLATEGRO script. But when I do the EM of the system the minimized system comes out at a very bad shape. I have

[gmx-users] SImulation error grompp

Hi All, I am running simulation of a system containing Coarse Grained 1SU4 (Minimized structure) and Coarse Grained DPPC lipid. I used the INFLATEGRO script to inflate the lipid and removed the overlapping lipids with proteins and then running the energy minimization. grommp says there are mismat

Re: [gmx-users] SImulation error grompp

I have updated the .top file as well after removing all the overlapping lipids from .gro file On Thu, Jan 14, 2010 at 10:15 AM, wrote: > Probably you removed lipids from the gro but not from the top (which you > need to do as well). > > Find a lipid atom name that occurs only once per molecule (

[gmx-users] Position Restrained Simulation for Coarse Grained DSPC

Dear All, I am trying to run the Position Restrained simulation for the Coarse Grained DSPC bi-layer. However, I am quite confused that how to generate the position restraint file for the CG atoms in lipid. Is there a difference between the position restraint file for the fine grained and coarse g

Re: [gmx-users] Position Restrained Simulation for Coarse Grained DSPC

the lipid right? Thanks On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Dear All, >> >> I am trying to run the Position Restrained simulation for the Coarse >> Grained DSPC bi-layer. However, I am quite confused