[gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 155
Sana Saeed
bioinformatic.lady at yahoo.com
Sat Feb 27 14:53:20 CET 2016
yes i used 2023 in the index file also. my distance restraints are one protein atom (atm num 120) and ligand atom 2023) but the error is about 2023, that it is out of range. may be the order of directive is incorrect. first i #include forcefield2nd #include ligand topology3rd protein topology contents4th distance restraints5th angle restraints6th dihedral restraints7th position restrain protein
Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.
On Saturday, February 27, 2016 5:40 PM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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Today's Topics:
1. renumber ligand atom numbers (Sana Saeed)
2. Re: renumber ligand atom numbers (Justin Lemkul)
3. Re: protein-DNA complex (Justin Lemkul)
4. Re: Using longer cut-off for AMBER99SB (Justin Lemkul)
5. Re: renumber ligand atom numbers (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Sat, 27 Feb 2016 11:04:19 +0000 (UTC)
From: Sana Saeed <bioinformatic.lady at yahoo.com>
To: Discussion List for GROMACS Users <gmx-users at gromacs.org>
Subject: [gmx-users] renumber ligand atom numbers
Message-ID:
<960643320.206067.1456571059662.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8
?hii am performing protein ligand binding free energy calculation through alchemical pathway. i made both topologies and generated distance, dihedral and angle restraints. in the index file i defined the restrained atoms. the error i got in energy minimization grompp is that the atom is out of range. it is because my protein is starting from atom num 1 and also my ligand starts with 1. in the gro file the numbering is changed , protein starts with 1 and ends with 1020 , and ligand starts after 1020. but in topology i included the ligand.itp (from acpype) into complex topology file, and both molecules starts with 1. how can i change the numbering of ligand atoms as in gro file. pdb2gmx -renum is not working because it is small ligand not a protein or peptide. if there is any code or any program please suggest. thanks in advance.?Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, Sou
th Korea.
------------------------------
Message: 2
Date: Sat, 27 Feb 2016 07:14:04 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org, Sana Saeed <bioinformatic.lady at yahoo.com>
Subject: Re: [gmx-users] renumber ligand atom numbers
Message-ID: <56D1930C.8000501 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 2/27/16 6:04 AM, Sana Saeed wrote:
> hii am performing protein ligand binding free energy calculation through
> alchemical pathway. i made both topologies and generated distance, dihedral
> and angle restraints. in the index file i defined the restrained atoms. the
> error i got in energy minimization grompp is that the atom is out of range.
> it is because my protein is starting from atom num 1 and also my ligand
> starts with 1. in the gro file the numbering is changed , protein starts with
No, grompp is complaining because (I'm guessing, since you haven't provided us
with an exact error message) you're specifying a completely nonexistent atom
number somewhere.
> 1 and ends with 1020 , and ligand starts after 1020. but in topology i
> included the ligand.itp (from acpype) into complex topology file, and both
> molecules starts with 1. how can i change the numbering of ligand atoms as in
Don't alter the topology numbering. It is a different concept from number in a
coordinate file. All [moleculetype] definitions MUST start from 1. If you
alter it, grompp will fail for a different reason. Sort out the grompp problem
you have now, not the one you'll create by breaking your topology.
-Justin
> gro file. pdb2gmx -renum is not working because it is small ligand not a
> protein or peptide. if there is any code or any program please suggest.
> thanks in advance. Sana Saeed Khan,Teaching-Research
> AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of
> BioinformaticsSoongsil University, Seoul, South Korea.
>
--
==================================================
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: 3
Date: Sat, 27 Feb 2016 07:16:19 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org, Mahboobeh Eslami
<mahboobeh.eslami at yahoo.com>
Subject: Re: [gmx-users] protein-DNA complex
Message-ID: <56D19393.8020102 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 2/27/16 3:03 AM, Mahboobeh Eslami wrote:
> hi all I want to do molecular dynamics simulations on protein-DNA complex.
> should the simulation of protein-DNA complex be done like the
> protein-protein complex? or is it better to select different force field for
> protein and DNA separately in MD simulation of protein-DNA? How is simulated
> protein-DNA complex? Thanks so much for your help.
>
It's just like simulating any other molecule-in-water system, be it a single or
multiple proteins. You shouldn't choose different force fields, because mixing
and matching is generally a very (very very very) bad idea. All modern
biomolecular force fields support proteins, DNA, and more. Read up on the
quality of each before moving on; for instance, the AMBER implementations in
GROMACS rely on very outdated AMBER nucleic acid force fields, and should be
replaced with the more recent parameter sets. I believe some of these are
available on the GROMACS user contributions page, but the validation issues,
AFAIK, were never resolved, so check carefully...
-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: 4
Date: Sat, 27 Feb 2016 07:18:46 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Using longer cut-off for AMBER99SB
Message-ID: <56D19426.2040606 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 2/26/16 2:22 PM, Agnivo Gosai wrote:
> Dear Users,
>
> I have checked in the forum about posts using longer cut-off against those
> used in the original force-field paper.
> I am using AMBER99SB ff (Hornak et al. 2006) and the ff paper says "A
> cutoff of 8-? was used for nonbonded interactions, and long-range
> electrostatic interactions were treated with the particle mesh Ewald (PME)
> method."
>
> In my simulations, I have used
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cels
> nstlist = 5 ; 10 fs
> rlist = 1.4 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.12 ; grid spacing for FFT
>
> So the cut-offs for non bonded interactions are much larger in my case. I
> used a longer cut-off thinking that it would be more accurate. But, in some
> of the earlier gromacs forum post I find that it is not required.
>
Cutoffs are part of the force field. If I had a nickel for every time I said
that...
Replace the phrase "not required" with "not ever recommended without strong
demonstration and justification that you're not breaking anything" and you'd be
right.
> So, if I need to satisfy reviewer comments then do I need to show
> equivalent simulation data as in the original ff paper.
>
You should repeat at least a subset of your simulations with the correct cutoffs
and (hopefully) demonstrate that the ensemble average properties do not differ
significantly. Depending on how many different types of systems you simulated,
this may be a fair amount of work, reinforcing the importance of getting it
right the first time :)
-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: 5
Date: Sat, 27 Feb 2016 07:40:08 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: Sana Saeed <bioinformatic.lady at yahoo.com>, Discussion list for
GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] renumber ligand atom numbers
Message-ID: <56D19928.7060300 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Please keep the discussion on the mailing list.
On 2/27/16 7:34 AM, Sana Saeed wrote:
> (Sorry i mentioned atom number 1 in first reply)
> i want to apply distance restrain on the ligand atom number 3, but this atom
> number also exist in protein?? so is it okay to specify atom number3 or should i
> use the numbering of that atom from gro file, because its different (atom number
> 2023) in gro file and index file from topology file. which numbering should i
> consider.
If this is in relation to your [intermolecular_interactions] then the numbers
specified there are the global atom numbers *from the coordinate file* and have
no relation to the individual topologies. So atom 3 is unambiguously defined as
that of the protein, and you must use 2023.
-Justin
> Sana Saeed Khan,
> Teaching-Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
> On Saturday, February 27, 2016 5:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 2/27/16 6:04 AM, Sana Saeed wrote:
> > hii am performing protein ligand binding free energy calculation through
> > alchemical pathway. i made both topologies and generated distance, dihedral
> > and angle restraints. in the index file i defined the restrained atoms. the
> > error i got in energy minimization grompp is that the atom is out of range.
> > it is because my protein is starting from atom num 1 and also my ligand
> > starts with 1. in the gro file the numbering is changed , protein starts with
>
> No, grompp is complaining because (I'm guessing, since you haven't provided us
> with an exact error message) you're specifying a completely nonexistent atom
> number somewhere.
>
> > 1 and ends with 1020 , and ligand starts after 1020. but in topology i
> > included the ligand.itp (from acpype) into complex topology file, and both
> > molecules starts with 1. how can i change the numbering of ligand atoms as in
>
> Don't alter the topology numbering. It is a different concept from number in a
> coordinate file. All [moleculetype] definitions MUST start from 1. If you
> alter it, grompp will fail for a different reason. Sort out the grompp problem
> you have now, not the one you'll create by breaking your topology.
>
> -Justin
>
>
> > gro file. pdb2gmx -renum is not working because it is small ligand not a
> > protein or peptide. if there is any code or any program please suggest.
> > thanks in advance. Sana Saeed Khan,Teaching-Research
> > AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of
> > BioinformaticsSoongsil University, Seoul, South Korea.
>
> >
>
> --
> ==================================================
>
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>
--
==================================================
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
==================================================
------------------------------
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