[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 109
kamakshi sikka
kamakshi.sikka at gmail.com
Sat May 28 08:09:37 CEST 2016
Dear Justin,
Charmm GUI created the topology file for the membrane only..I am asking for
C-terminal amidated peptide topology file. pdb2gmx command does not give
topology file here because of C-terminal amide residue which is missing in
the residue database. Please help.
Regards
Kamakshi Sikka
On Fri, May 27, 2016 at 8:40 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. NMA problems with mass-weighting -m option (Ravasio Riccardo)
> 2. NEMD (khourshaeishargh at mech.sharif.ir)
> 3. Re: Lipid Head group Orientation (Chandan Choudhury)
> 4. Re: NEMD (Mark Abraham)
> 5. Output of g energy (khourshaeishargh at mech.sharif.ir)
> 6. Re: amidated C-terminal residue of peptide (Justin Lemkul)
> 7. Re: Distance restraint and pull code (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 27 May 2016 13:49:17 +0000
> From: Ravasio Riccardo <riccardo.ravasio at epfl.ch>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] NMA problems with mass-weighting -m option
> Message-ID: <1464356957471.73393 at epfl.ch>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx users,
>
>
> After performing Normal Mode Analysis, I would like to print a non
> mass-weighted spectrum, but both with option -m false and with -m true I
> get mass-weighted eigenvalues and eigenvectors. Why? I'm using version
> 5.1.2. I looked at the source code, but it was of version 3.2.0: maybe the
> -m option was forgotten in the last version? Or, what am I doing wrong?
>
>
> I'm using the usual following commands:
>
>
> gmx_d grompp -v -f nma.mdp -c $STRUCT-vacuum-min$((sample-1)).gro -p
> $STRUCT.top -o $STRUCT-vacuum-nma.tpr
>
>
> gmx_d mdrun -v -s $STRUCT-vacuum-nma.tpr -mtx $STRUCT-vacumm-nma.mtx
>
>
> gmx_d nmeig -f $STRUCT-vacumm-nma.mtx -s $STRUCT-vacuum-nma.tpr -m true
> -last 3693
>
>
> I tried to put also 0/1 or yes/no, but nothing changes.
>
>
> I thank you for your kindness and for your help.
>
>
> Best regards,
>
>
> Riccardo
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 27 May 2016 18:20:12 +0430
> From: khourshaeishargh at mech.sharif.ir
> To: gmx-users at gromacs.org
> Subject: [gmx-users] NEMD
> Message-ID:
> <c5e93e512fa8a17c53c47a38efda8faa.squirrel at mech.sharif.edu>
> Content-Type: text/plain;charset=UTF-8
>
> Dear Gromacs users
> I am a M.Sc student at Sharif university in field of mechanical
> engineering. for my M.Sc thesis I'm using GROMACS and for a part of it, I
> need to use NEMD. I searched Internet but unfortunately found nothing
> related to gromacs ( I mean Example, article and ...). So could anyone
> please
> introduce me something relevant to NEMD part of GROMACS like tutorial,
> article or anything else?
> I really appreciate it.
>
> best regards, Ali
>
> ==================
>
> Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
>
> Department of Mechanical Engineering
>
> Sharif University of Technology, Tehran, Iran
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 27 May 2016 10:33:29 -0400
> From: Chandan Choudhury <iitdckc at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Lipid Head group Orientation
> Message-ID:
> <
> CAHESojwzBp-pMyX-GHSmHGeBhC16hm3qRaepLYC9KY-h5wBTFw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Nidhin!
>
> I wrote a code some time ago on the the orientation of lipid molecules
> which was the specific to the problem addressed at
> http://pubs.acs.org/doi/full/10.1021/bm4011408. If you need, I can share.
>
> Chandan
>
> On Thu, May 26, 2016 at 7:50 PM, Nidhin Thomas <
> nidhin.thomas0624 at gmail.com>
> wrote:
>
> > Hi GROMACS Users,
> >
> > This question was asked before in the forum. But I could not find a
> > complete answer. So I?m asking again. Is there any command in GROMACS
> that
> > can give the orientation of lipid head groups of all lipids averaged over
> > time?
> >
> > I wrote a code which takes the co-ordinates of P and N atoms at each time
> > frames and gives the orientation of P-N vector averaged over the time. I
> > was wondering if there is any command in GROMACS that can provide this
> data
> > directly ?
> >
> > I used g_sgangle command to obtain the angles of one lipid molecule. But
> > how do we get the data for all lipids in one file?
> >
> > Thanks,
> > Nidhin Thomas
> > University of Houston
> > --
> > 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.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
>
>
>
>
> --
>
> Chandan Kumar Choudhury
> Post Doctoral Fellow
> Clemson University
> South Carolina
> USA
>
> *"All work and no play makes Jack a dull boy...?*
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 27 May 2016 14:46:42 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] NEMD
> Message-ID:
> <
> CAMNuMATbB-Dk8GX-EMLTNKGKpKRPMpn8wNUVn0DD3U+vMCS9bg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> That's a pretty open-ended inquiry. You might find more people if you
> narrow it down a bit.
>
> Mark
>
> On Fri, May 27, 2016 at 4:23 PM <khourshaeishargh at mech.sharif.ir> wrote:
>
> > Dear Gromacs users
> > I am a M.Sc student at Sharif university in field of mechanical
> > engineering. for my M.Sc thesis I'm using GROMACS and for a part of it, I
> > need to use NEMD. I searched Internet but unfortunately found nothing
> > related to gromacs ( I mean Example, article and ...). So could anyone
> > please
> > introduce me something relevant to NEMD part of GROMACS like tutorial,
> > article or anything else?
> > I really appreciate it.
> >
> > best regards, Ali
> >
> > ==================
> >
> > Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
> >
> > Department of Mechanical Engineering
> >
> > Sharif University of Technology, Tehran, Iran
> > --
> > 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.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 27 May 2016 19:04:21 +0430
> From: khourshaeishargh at mech.sharif.ir
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Output of g energy
> Message-ID:
> <1aa2b473ae83ce403881dfaa175bb579.squirrel at mech.sharif.edu>
> Content-Type: text/plain;charset=UTF-8
>
> Dear GROMACS user
> I have a question about the output of g energy. what is exactly the
> meaning of Pressure x-x ? is it the same as the stress in mechanical
> engineering or not ?!
> best regards, Ali
>
> ==================
>
> Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
>
> Department of Mechanical Engineering
>
> Sharif University of Technology, Tehran, Iran
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 27 May 2016 11:09:12 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] amidated C-terminal residue of peptide
> Message-ID: <af6ea19b-f316-ed27-9cb0-17b77c7d5c96 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/27/16 8:25 AM, kamakshi sikka wrote:
> > Hello all,
> >
> > I am doing membrane peptide simulation studies using POPS/POPC membrane
> > built by Charmm GUI. While generating the topology file for the amidated
> > peptide, I get a fatal error: '*Residue 'NHE' not found in
> > residue topology database'*. I am using Charmm36 force field here. Can
> you
> > please help me in solving this issue.
> >
>
> Let CHARMM-GUI build everything for you. It writes GROMACS topology and
> input
> files. There's no need to take anything back into pdb2gmx.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 27 May 2016 11:10:43 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Distance restraint and pull code
> Message-ID: <2f127ded-0ac6-3b2d-0a32-d447600ea345 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/26/16 9:20 PM, HongTham wrote:
> > Dear Gromacs users,
> > Im running a Zn bound protein - ligand complex system. Zn makes
> > coordinations with 3 HIS and NH- of ligand. in the itp file, Zn and
> protein
> > in the same [molecule] but not ligand. because it cant be applied
> distance
> > restraint ZN and ligand (they are belong to different [molecule]), I
> > applied distance restraint for ZN and 3 HIS, and used pull code to keep
> > ligand closed to ZN
> > This is the distance restrains assigment in topology file of ZN and
> > protein, while 3852 is ZN and other is HIS atoms.
> > [ distance_restraints ]
> > ; ai aj type index type low up1 up2 fac
> > 3852 1354 1 0 1 0.2 0.21 0.22 0.1
> > 3852 1390 1 0 1 0.2 0.21 0.22 0.1
> > 3852 1721 1 0 1 0.2 0.21 0.22 0.1
> >
> > The pull code in mdp file is like below, in which, a_3862 is N atom of
> > ligand
> > disre = simple ; distance restraints
> > disre_fc = 1000 ; Force constant
> > pull = umbrella
> > pull-ngroups = 2
> > pull-ncoords = 1
> > pull-group1-name = ZN
> > pull-group2-name = a_3862
> > pull-geometry = distance ; simple distance increase
> > pull-coord1-groups = 1 2
> > pull-dim = Y Y Y
> > pull-coord1-rate = 0.0 ; not pull, just distance restraint at a reference
> > distance bw 2 groups
> > pull-coord1-k = 1000 ; kJ mol^-1 nm^-2
> > pull-start = yes ; define initial COM distance > 0
> > pull-nstxout = 5000
> > pull-nstfout = 5000
> >
> >
> > It seemed the pull code worked well. The problem is the distance
> restraint
> > is not effective. ZN only can be kept closed to one of three HIS, and
> moves
> > far away from 2 others.
>
> Because you defined one restraint using the pull code. Either define
> multiple
> restraints or increase the strength of your distance restraints.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> --
> 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.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 145, Issue 109
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