[gmx-users] gromacs.org_gmx-users Digest, Vol 162, Issue 7
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Tue Oct 3 18:59:13 CEST 2017
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> Today's Topics:
>
> 1. Charges and Antechamber (ABEL Stephane)
> 2. Re: peptide ligand (farial tavakoli)
> 3. Re: grompp very slow generating .tpr when excluded bonded
> neighbours is large (Mark Abraham)
> 4. Re: Charges and Antechamber (Jo?o Henriques)
> 5. checking simulation progress (Bukunmi Akinwunmi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Oct 2017 15:10:33 +0000
> From: ABEL Stephane <Stephane.ABEL at cea.fr>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Charges and Antechamber
> Message-ID:
> <3E39B768BB199548AB18F7289E7534AF38818043 at EXDAG0-B0.intra.cea.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> HI
>
> It is quite easy to derive RESP charges and use them with GROMACS. You
> could follow the steps
>
> 1) Build a pdb file of your molecule/modified residue
> 2) Use the web server pyRED
> (http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and derive
> the RESP charges. The webserver will also give you all the necessary
> parameters of the ff (mol2 file, atom types, (non)bonded parameters)
> 3) Use these parameters to construct a rtp file for GROMACS for a given
> force field
> 4) and finally use pdb2gmx with the pdb file to obtain the itp file.
>
> That's all
>
> Good luck
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 3 Oct 2017 15:13:58 +0000 (UTC)
> From: farial tavakoli <farial.tavakoli at ymail.com>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] peptide ligand
> Message-ID: <1201432437.876905.1507043638717 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
> #715FFA solid !important; padding-left:1ex !important;
> background-color:white !important; } Thanks alot for your advxe
> I would really appreciate if you advice me more to split protein and
> ligand in index file, I saw the index help , but couldnt find out how
> should I use ? ?splitch? nr ? script to split them.?
> With best regardsFarial
gmx make_ndx -f em.gro -o index.ndx
then select protein ( in your case it will contain both the protein and
the peptide) and your ligand.
press q (save it)
now assemble your nvt tpr file using grompp ( pass here -n index.ndx)
It is explained very nicely in gromacs tutorial Protein - Ligand
(Equilibration section)
thank you
>
> Sent from Yahoo Mail for iPhone
>
>
> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
>
>
>
> On 10/3/17 9:17 AM, ?farial tavakoli? ? wrote:
>> Dear Justin
>>
>> Thank you so much for your reply.
>> You mean , I should generate a topology file for my complex instead of
>> creating topology for each of them separately ?
>>
>
> As long as the protein and peptide ligand are denoted as being in
> separate chains (different chain ID or use of TER in the PDB file), then
> pdb2gmx will do everything for you.
>
> -Justin
>
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Justin Lemkul <jalemkul at vt.edu>
>> *To:* gmx-users at gromacs.org; ?farial tavakoli? ?
>> <farial.tavakoli at ymail.com>
>> *Sent:* Tuesday, 3 October 2017, 16:35:49
>> *Subject:* Re: [gmx-users] peptide ligand
>>
>>
>>
>> On 10/3/17 4:26 AM, ?farial tavakoli? ? wrote:
>> > Dear GROMACS users
>> > I need to run a MD on my Protein-peptide ligand complex in GROMACS.
>> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
>> was Protein_chain_B) and converted it to .itp file to string it in
>> Protein.top file, then, added Protein_chain_B in [ molecules ]
>> directive to create one topology file for my complex. Created newbox
>> and solvate.
>>
>> You shouldn't have to do any topology manipulation. pdb2gmx handles
>> multiple
>> chains natively without any additional effort on your part.
>>
>> -Justin
>>
>>
>> > But when I gave this command:gmx grompp -f em_real.mdp -c
>> solv_ions.gro -p topol.top -o em.tpr
>> >
>> > I faced to this error:
>> >
>> > Group Protein_chain_B referenced in the .mdb file was not found in
>> the index file. Group names must match either [moleculetype] names or
>> custom index group names, in which case you must supply an index file
>> to the '-n' option
>> > of grompp.
>> >
>> > In spite of , my ligand [ moleculetypes ] in the ligand.itp file is
>> Protein_chain_B , but GROMACS gives error.
>> > Would you please advice me how can I solve this problem?
>> >
>> > Best
>> > Farial
>>
>> >
>> >
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>>
>> ==================================================
>>
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> 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
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> a mail to gmx-users-request at gromacs.org.
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 03 Oct 2017 15:37:31 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] grompp very slow generating .tpr when
> excluded bonded neighbours is large
> Message-ID:
> <CAMNuMATwCXNMaXV7wxrHjNH6o-Nz9vKPXVWtO41N+9mi8KJk1Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I'm sure we have opportunities to improve this code - please do file a
> redmine issue with repro inputs so we can profile and see!
>
> Thanks,
>
> Mark
>
> On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/2/17 11:14 PM, Dallas Warren wrote:
>> > Thanks for the reply Justin.
>> >
>> > I am just going to use the largest exclusion bond distance I can, then
>> > ignore the RDF of those beyond that distance.
>> >
>> > Seems curious to me (not actually understanding what grommp is
>> > generating) that the list is so large. These are linear molecules, 38
>> > atoms, 60 molecules in total.
>>
>> It generates a matrix of all possible exclusions, sorts them, then
>> removes
>> duplicates. So for nrexcl = 37 you need memory on the order of 37 * 37 *
>> 60 * (2
>> * sizeof(int)) - the factor of 2 for the atom numbers comes from the
>> fact
>> that
>> you're actually allocating an array of type "sortable" which is a pair
>> of
>> atom
>> numbers.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>> --
>> 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: 4
> Date: Tue, 3 Oct 2017 17:41:27 +0200
> From: Jo?o Henriques <joao.m.a.henriques at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charges and Antechamber
> Message-ID:
> <CAHv45qPTFJMwRjoXxBYU-EGxU6toR2ZmZWq=7eQ14gC9v_A0pQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Or this... :) I've never used it, but I'm sure it works like a charm. I
> personally prefer to be more involved in all stages of the process, but
> I'm
> a bit old school and I like to avoid "black boxes" for my own learning
> benefit. That being said, I'm sure it does the job and it's faster &
> simpler. It's probably the best way to go for someone with less experience
> with this sort of task.
>
> Cheers,
>
> J
>
> On Oct 3, 2017 5:10 PM, "ABEL Stephane" <Stephane.ABEL at cea.fr> wrote:
>
> HI
>
> It is quite easy to derive RESP charges and use them with GROMACS. You
> could follow the steps
>
> 1) Build a pdb file of your molecule/modified residue
> 2) Use the web server pyRED (http://upjv.q4md-
> forcefieldtools.org/REDServer-Development/) and derive the RESP charges.
> The webserver will also give you all the necessary parameters of the ff
> (mol2 file, atom types, (non)bonded parameters)
> 3) Use these parameters to construct a rtp file for GROMACS for a given
> force field
> 4) and finally use pdb2gmx with the pdb file to obtain the itp file.
>
> That's all
>
> Good luck
> --
> 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: Tue, 3 Oct 2017 16:03:01 +0000
> From: Bukunmi Akinwunmi <bukunmi.akinwunmi at uef.fi>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] checking simulation progress
> Message-ID:
> <HE1PR01MB2940456C37826A4807AAAE1385720 at HE1PR01MB2940.eurprd01.prod.exchangelabs.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> dear gmx-users,
> my simulation has been running for sometime but now I want to know how
> long is left for the simulation to be completed. I need help with the
> command to analyse a running simulation.
>
> Best regards,
> Bukunmi
>
>
> ------------------------------
>
> --
> 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
>
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> 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 162, Issue 7
> *****************************************************
>
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