Re: [gmx-users] Acetylation of lysine

On Wed, Jan 24, 2018 at 11:58 AM, Shraddha Parate wrote: > [sp@atp 2RTU_Gromos45a3]$ gmx pdb2gmx -f 2RTU_1.pdb -o 2RTU.gro -water > spce > GROMACS:gmx pdb2gmx, VERSION 5.0.6 > > GROMACS is written by: > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar > Aldert van Buur

Re: [gmx-users] Acetylation of lysine

[sp@atp 2RTU_Gromos45a3]$ gmx pdb2gmx -f 2RTU_1.pdb -o 2RTU.gro -water spce GROMACS:gmx pdb2gmx, VERSION 5.0.6 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit Groen

Re: [gmx-users] Acetylation of lysine

[sp@atp 2RTU_Gromos45a3]$ gmx pdb2gmx -f 2RTU_1.pdb -o 2RTU.gro -water spce GROMACS:gmx pdb2gmx, VERSION 5.0.6 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit Groen

[gmx-users] gangle for a plane and z axis

Hi Gromacs users, I would like to calculate the angle distribution between a plane and z axis using gangle. In a 5-member ring, there are three atoms of O1-C-O2 which form an angle. So, I will choose these three atom names to define the plane. I am not sure how the g_angle makes the vector norma

[gmx-users] How to solve this fatal error?

Dear all l am using gromacs 4.5.5 version for simulation carbon nanotubes with charmm27 force feild ,there was no error grompp stage,but when l do simulation of carbon nanotube in tip3p water encountered with fatal error: [ file tip3p.itp, line 40]: Atom index (1) in settles out of bounds (1

Re: [gmx-users] 2016.3 only gmx grompp error on NVT step for ions

On 1/23/18 12:21 PM, Sarai G wrote: ​Hello Justin, Sorry about the subject line, I fixed it this time around. I have the .itp files (toppar folder) and the .top files as you requested as well as a larger tar.gz which all of the files produced in the testing run within it. The error message

Re: [gmx-users] rlist- group scheme

Hi Mark, thanks for remarks, just one point: > > But what I see from resulted potential vs > > displacement of two molecules, is that Gromacs has taken the potential to > > zero at rlist not *''rcut-off''*. That is why for rcut-off > rlist the > > result is not correct. > > > > You're seeing the

Re: [gmx-users] 2016.3 only gmx grompp error on NVT step for ions

​Hello Justin, Sorry about the subject line, I fixed it this time around. I have the .itp files (toppar folder) and the .top files as you requested as well as a larger tar.gz which all of the files produced in the testing run within it. Sarai > Date: Tue, 23 Jan 2018 12:04:08 -0500 > From: J

Re: [gmx-users] rlist- group scheme

Hi, On Tue, Jan 23, 2018 at 1:31 PM Faezeh Pousaneh wrote: > > > > > > > > > For any range of cut off it gives wrong results for rlist>rcut-off. > > > > > > Now I understand where the problem comes. I tried to see the > collisions > > of > > > two molecules with a table (user potential). > > >

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 117

On 1/23/18 12:02 PM, Sarai G wrote: ​Hello, Line 14 relates to the ions, not the QS21. In all runs and testing, the error was always relating to the ions. Different systems both with and without ions were created using QS21 and other molecules and the error only appeared when there were ions i

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 117

​Hello, Line 14 relates to the ions, not the QS21. In all runs and testing, the error was always relating to the ions. Different systems both with and without ions were created using QS21 and other molecules and the error only appeared when there were ions involved. Ensuring that the reference lin

Re: [gmx-users] Acetylation of lysine

On 1/23/18 11:51 AM, Shraddha Parate wrote: These lines right here point the the exact problem: Warning: Residue KAC31 in chain has different type (Other) from starting residue GLY1 (Protein). Warning: Residue KAC32 in chain has different type (Other) from starting residue GLY1 (Protein). Warn

Re: [gmx-users] Acetylation of lysine

Using the Gromos45a3 force field in directory ./gromos45a3.ff Opening force field file ./gromos45a3.ff/aminoacids.r2b Reading 2RTU_1.pdb... WARNING: all CONECT records are ignored Read 715 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 cha

Re: [gmx-users] Please provide some advice on my simulations

Hi, The code isn't designed to produce reproducible trajectories, and generally you should not want that. See http://www.gromacs.org/Documentation/Terminology/Reproducibility. You should also consider the characteristic timescales of the thing you want to observe. If an unexpected event has occurr

Re: [gmx-users] 2016.3 only gmx grompp error on NVT step for ions

Hi, This is a new warning in that recent version of GROMACS, because we found that constraints = all-bonds could produce artefacts. The error message points out line 14 of your topology, which presumably relates to the QS21 molecule topology, not the ions. So it's probably triggered by one of the

[gmx-users] 2016.3 only gmx grompp error on NVT step for ions

Greetings and Salutations, ​ 1qs21-test_log ​​ 1qs21_nvt.mdp ​​ qs21_testNVT.mpg

[gmx-users] Please provide some advice on my simulations

Dear gromacs users, I have performed simulation for RNA bound protein complex (35 atoms). however within 10ns i have observed unusual large movement of N-terminal region and shows interaction with dsRNA, which may not be possible, however I have run simulations for 100ns. In order to check the

Re: [gmx-users] Atom OT1 in the residue

Dear Justin, Thank you very much your help. Best regards, Miji > -- > > Message: 2 > Date: Tue, 23 Jan 2018 06:44:59 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Atom OT1 in the residue > Message-ID: <82fdffdd-85b4-56ab-8445-27f

Re: [gmx-users] SDS initial setup

On 1/23/18 9:29 AM, za...@tezu.ernet.in wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via e

Re: [gmx-users] Acetylation of lysine

On 1/23/18 10:15 AM, Shraddha Parate wrote: Hi Justin, I get the same error even after defining the residue KAC as Protein in residuetypes.dat Please provide the full screen output from pdb2gmx (not just the warnings). There are often clues in there as to what's going on. -Justin --

Re: [gmx-users] Acetylation of lysine

Hi Justin, I get the same error even after defining the residue KAC as Protein in residuetypes.dat Regards, Shraddha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.o

[gmx-users] SDS initial setup

> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'h

Re: [gmx-users] Errors while building with Cuda 9.0

Hi, You really should update to 2016.4, but if you for som reason can not, you can pass the target CUDA architectures to CMake; see GMX_CUDA_TARGET_SM documented here: http://manual.gromacs.org/documentation/2016.4/install-guide/index.html#cuda-gpu-acceleration -- Szilárd On Tue, Jan 23, 2018 a

Re: [gmx-users] rlist- group scheme

> > > > > For any range of cut off it gives wrong results for rlist>rcut-off. > > > > Now I understand where the problem comes. I tried to see the collisions > of > > two molecules with a table (user potential). > > > Over what range is your interaction defined? If the potential isn't zero by > th

Re: [gmx-users] Rupture force definition

On 1/23/18 3:01 AM, Rakesh Mishra wrote: Ok, thanks for learifivcation. Dear Justin I have one another query regarding pulling using umbrella sampling. See these two lines below. Eg.Pull group natomspbc atom distance at startreference at t=0 131

Re: [gmx-users] Acetylation of lysine

On 1/22/18 9:58 PM, Shraddha Parate wrote: Dear Gromacs Users, I need to perform acetylation of lysine residues in my work for which I have acetylated the lysine (KAC) from Vienna PTM server. I came across a paper titled 'A Systematic Framework for Molecular Dynamics Simulations of Protein Pos

Re: [gmx-users] Atom OT1 in the residue

On 1/23/18 1:59 AM, Мижээ Батсайхан wrote: Dear gmx user, I am using gromacs 5.1 with charmm36-march2017 force field. I have an error as following: "Atom OT1 in residue DTRP 4 was not found in rtp entry DTRP with 24 atoms while sorting atoms." How can I fix this error? Additionally, I modif

Re: [gmx-users] Osmotic Pressure Calculations and fixed reference values

Dear Dr. Justin, Thanks for the clarification and sorry for the delayed response from my side. I am calculating flat bottom potential along with osmotic pressure values to verify my calculations. The flat bottom potential values calculated by in-house code matches with g_energy values. Thanks again

Re: [gmx-users] Atom OT1 in the residue

On Tue, 23 Jan 2018 at 3:59 PM, Мижээ Батсайхан wrote: > Thank you for your answer. I modified the L-TRP structure to D-TRP > structure, and the last version of charmm36 contains a topology of D-TRP. I > used that one. Check for the naming of OT1 in the residue topology database of Dtrp > > T

Re: [gmx-users] Atom OT1 in the residue

Thank you for your answer. I modified the L-TRP structure to D-TRP structure, and the last version of charmm36 contains a topology of D-TRP. I used that one. Thanks. > > Dear gmx user, > > > > I am using gromacs 5.1 with charmm36-march2017 force field. I have an > error > > as following: > > >

Re: [gmx-users] MDP define in GROMACS 2018

Hi, On Mon, Jan 22, 2018 at 7:41 AM Joshua Mitchell wrote: > Hi all, > > I am excited to try out the new PME code in GROMACS 2018! It seems that > preprocessor variables can no longer be given values in the MDP as of > GROMACS 2018? So in 2016 I could do > > define = -DPOSRES -DPOSRESFC=500.0 >

Re: [gmx-users] rlist- group scheme

Hi, On Mon, Jan 22, 2018 at 10:25 AM Faezeh Pousaneh wrote: > For any range of cut off it gives wrong results for rlist>rcut-off. > > Now I understand where the problem comes. I tried to see the collisions of > two molecules with a table (user potential). Over what range is your interaction d

Re: [gmx-users] Rupture force definition

Ok, thanks for learifivcation. Dear Justin I have one another query regarding pulling using umbrella sampling. See these two lines below. Eg.Pull group natomspbc atom distance at startreference at t=0 131 1387 231