[gmx-users] the aggregation of a peptide using gromacs

Dear all I want to survey the aggregation of a peptide using molecular dynamics simulation, please let me know there is a tutorial to assess the aggregation of related peptide? I'm looking forward to getting your answer. Thanks a lot. Best wishes -- *Marzieh DehghanPhD of BiochemistryInstitut

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 84

.4 (Abhishek Acharya) >2. Re: Error: Cannot set thread affinities on the current > platform (Neena Susan Eappen) >3. Re: Error: Cannot set thread affinities on the current > platform (Benson Muite) >4. free binding ene

[gmx-users] free binding energy calculation

Dear all I want to calculate free energy calculation under gromacs 5.1.4 and used the following link "*http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/04_EM.html "* wh

[gmx-users] dssp excutable-error

Dear all I installed dssp software on ubuntu version 12.04 in the /usr/local/bin, when I run the following command "*sudo find / -name dssp*" it showed the mentioned pathway, but when I apply the following comand "*gmx do_dssp -f xtc -s tpr -o xpm -sc xvg -tu ns*" I confronted to this error: *"fai

[gmx-users] excutable dssp

Dear all I installed dssp on the gromacs version 5.1.4 and setenv as the following command: *export dssp=/usr/local/bin/gromacs/do_dssp* dssp was started to analyzed the protein structure, but after several minutes, we confront to this error: *failed to execute command, try specifying your dssp

[gmx-users] csh REAME error in gromacs

Hi Dear all I prepared a cell membrane using charm GUI, but when I run csh README in terminal to optimize constructed membrane, I confronted to the following error: Can not open file: step7_4.tpr Can not open file: step7_5.tpr .. Can not open file: step7_10.tpr please let me know how to so

[gmx-users] adding missing hydrogen using pdb2gmx

Hi Dear all I want to add missing hydrogen to the related protein structure using pdb2gmx, but I don't know how to solve this problem. please let me know how to add hydrogen to all residues in the pdb file like the following sample: ATOM 17 N LEU A 2 24.961 35.448 12.600 1.00 0.0

[gmx-users] cgenff charm error

Hi Dear all I used charm36 and cgenff (http://mackerell.umaryland.edu/charmm_ff.shtml) to convert str format of ligand to itp format. when I used the following command: python cgenff_charmm2gmx.py LIG lig.mol2 lig.str charmm36-jul2017.ff/ I confront this error: NOTE1: Code tested with python 2.

[gmx-users] fatal error in read a checkpoint file

Hi Dear all I want to do MD run using gromacs, but I confront to the mentioned error "attempting to read a checkpoint file of version 17 with code of version 16" please let me know how to solve this problem. I am looking forward to getting your answer. thanks a lot. -- *Marzieh DehghanPhD

[gmx-users] POPG/POPE membrane

Hi Dear all, I want to simulate the combination of POPG/POPE membrane with a ratio 3:1 using gromacs. I would like to know is there any tutorial to use for making the mentioned mix membrane? I am looking forward to getting your answer, Thanks a lot, Marzieh -- *Marzieh DehghanPhD of Biochemis

[gmx-users] covariance map for all residues

Hi Dear all I want to draw covariance map using gromacs, so I have two questions: 1- I used the following command,but x and y axis show based on atom: gmx covar -s md.tpr -f md.trr -o eigenval.xvg -v eigenvect.trr -xpma covara.xpm the number of atoms on the x and y axis is less than total atom

[gmx-users] elevation the temperature

Hi Dear all I want to elevate the temperature of my simulation system with the rate of 1 K/ns, so I would like to know which parameter should be changed to elevate the temperature from 300 up to 450 K? thanks a lot best wishes -- *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry a

[gmx-users] dssp plot

Hi Dear all I used dssp plot to show the alteration of secondary structure for special residue numbers such as 100-200, but after calculation them, y axis of dssp plot is started from zero instead from 100. please let me know which part of m2p file should be changed to solve this problem. thanks

[gmx-users] how to generate a trr file

Dear all Hi I performed molecular dynamics simulation during 100 ns, but now I want to create a trr or xtc file including 50 ns. how I can generate trajectory file containing 50 ns from 100 ns of MD run? thanks a lot best wishes -- *Marzieh DehghanPhD of BiochemistryInstitute of biochemistr

[gmx-users] membrane simulation

Hi Dear all I have a protein with three parts: inter-membrane, transmembrane, outer-membrane regions I want to simulate this protein into a membrane, please let me know how to set this protein into the membrane which for example the amino acids located in outer-membrane and the exact amino acids

[gmx-users] error in phosphoserine simulation during MD

thank you very much I tried to complete pdb file, but since pdb file containing phosphoserine which is different from its sequence, because there is serine in its sequence file, when I wanted to use modeller, I confronted these error " sequence difference between alignment and pdb. I used another

[gmx-users] error in phosphoserine simulation during MD

Hi Dear Justin Thanks a lot for your kind answer, I applied two types of command to get rid of the previous error *at first*, the following command was used: *gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc * but I confronted these error CYS901 SG7090 1.414 CYS905 SG7117

[gmx-users] error in phosphoserine simulation during MD

Hi Dear all I want to simulate a protein containing phosphoserine using MD, so I place the force field into the working directory and modified all parameters of force field for example SEP (phosphoserine) was added as Protein in the residuestypes.dat , but I confronted the following error? Atom

[gmx-users] coordination atoms of ion

Hi every body I have a protein which contains 6 calcium ions. after running MD with gromacs, output file resulting from MD superimpose input file. it showed calcium ions weren't in their origin coordinate. I would like to define coordination atoms for calcium ions. please let me know how I can so

[gmx-users] nvt equilibration; error

Hi Dear Justin thanks a lot for your kind answer after creating a topology file using topolbuild, all parameters such as information about bond, angle, . . . were completed based on ffbond.itp. then I used topol file to held energy minimization by gromacs and after holding NVT command, I confront

[gmx-users] nvt equilibration: error

Hi Deat Justin I formed a covalent bond according to the following steps: 1- Covalent bond was formed between insulin and glucose by hyperchem 2- Topology file was created using topolbuild *PS:* I checked topology file, it showed all atoms i.e, protein and ligand were called as UN

[gmx-users] nvt equilibration

Hi thank you for your answer I used the following instructions: make_ndx -f em.gro -o index.ndx and appear thses text: Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 421 Other residues There are: 4446 Water residues There are:10

[gmx-users] error group protein not found

Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names

[gmx-users] install xmgrace on centos 6.5

Hi after finishing MD run, I wanted to analyze the results, so I should install grace on centos 6.5, I wrote the following command: yum install grace but I confronted this error "nothing to do". please let me know, what I can solve this problem? thanks a lot -- *Marzieh DehghanPhD Candi

[gmx-users] there wasn't md_0_1.xtc file

Hi every body I have two questions? 1- accroding to the previos email, I used gromacs to run a covalent bond, for the first try,I run my covalent bond based on the tutorail (lysozyme in water) that nstxtcout = 0 was in md.mdp file, so I changed nstxtcout =0 to >0 and run was repeated. in the both

[gmx-users] there wasn't md_0_1.xtc file

Hi every body after creating a covalent bond, I ran output file based on GROMACS tutorial (Lysozyme in water) and applied the following command " mdrun -deffnm md_0_1". at the end of 1ns, I achieved the following output files: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_

[gmx-users] topology include file "gmx43a1.ff/ffG43a1.itp " not found

Hi every body I want to perform molecular dynamics using gromacs for a covalent bond, so I used topol build to create a topology file. after holding the following command: grompp -f ions.mdp -c test.gro -p test.top -o ions.tpr I confronted this error: topology include file "ffG43a1nb.itp" not fo

[gmx-users] topolobuild error

Hi after making a topology file using topolbuild and hold the following command using gromacs: grompp -f ions.mdp -c test_solve.gro -p test.top -o ions.tpr I changed fftest.itp and topology file resulting from topolobuild to : fftest.itp: # include "oplsaa.ff/ffnonbonded.itp" topology file: #

[gmx-users] ffbond.itp

Hi every body 1- In the phosphate group, we have 4 oxygen atoms that bond to the phosphate. Two of them are as follow: CH2-O-P-OH and the others include: - A double bond is on the top of phosphor atom - A OH group is at the bottom of phosphor atom We put the atom type of

[gmx-users] ffbond.itp

Hi every body *in order to complete ffbond.itp for new covalent bond, we use the following article A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field **Parameter Sets 53A5 and 53A6",but we can't find out how to solve these problems?* *1-Gromos a

[gmx-users] how can we modify *.rtp file? (again)

f gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. recovering topology from tpr (Rebeca Garc?a Fandi?o) >2. Re: QM/MM excited state optimization (xiao) >3. Re: recovering topology from tpr (Mark Abraham) >4. how can we modify *.rtp file? (marzieh

[gmx-users] how can we modify *.rtp file?

Hi every body we would like to simulate a covalent modification on a protein by gromacs. Based on gromacs tutorial, modification is introduced as a new amino acids, so we changed *.rtp file. As a trick, we used parameters in output file (*.top) of topolbuild and prodrug server to modify the *.rtp

[gmx-users] adding a new residue into an existing force field?

Hi according to the previous email, since I want to keep covalent bond during the MD using gromacs, you said me, I should add a new residue into an existing force field , but I have two questions? 1- based on the gromacs website , I ca

[gmx-users] constrained bonds

Hi every body I created covalent bond by the latest version of autodock.according to the tutorial of protein-ligand complex with gromacs, the result of covalent bond was used for MD. after energy minimization, ligand was separated from protein. I would like to know how can I occur constrained bo

[gmx-users] mdrun in gromacs 5.0.2

hi every body After installing gromacs 5.0.2, when I write mdrun or gmx pdb2gmx . . . , I confronted the following error: command not found but mdrun has been installed in /usr/local/gromacs/bin. Please let me know how can I correct this error? Thanks a lot Best woshes -- Gromacs Users mailing li

[gmx-users] topolbuild

Hi I used topolbuild to create topology file for glycated insulin, but there are several dihedral parameters which are empty in output file. in order to complete output file, several servers were used such as ATB, vienna, unfortunately none of them couldn't help me. I would like to know how

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 121, Issue 12

anaging the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. topolbuild err

[gmx-users] topolbuild error

Hi after making topology file by using topolbuild, we used the following command in the gromacs: grompp -f em.mdp -c test_solv.gro -p test.top -o ions.tpr we confronted the following error: topology include file "ffoplsaanb.itp" not found would like to know how can I solve this problem? thanks

[gmx-users] glycated insulin (GROMACS)

Dear Justin Hi after glycation insulin by autodock, I wan to run it by GROMACS. I would like to know is it possible and correct? best regards thanks a lot marzieh -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran-

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 32

duplicates. >>>>> Now there are 258 residues with 4071 atoms >>>>> Chain time... >>>>> >>>>> Back Off! I just backed up protein_Protein_chain_A.itp to >>>>> ./#protein_Protein_chain_A.itp.7# >>>>> Making bonds... >>>>> Number of bonds was 4134,