Re: [gmx-users] lower-end GPUs

[Alex]

Thanks, this is very useful! I was looking at the 1080 and the pricing 
is fairly acceptable.


Will keep in mind about CR version. Actually, we wouldn't be buying 
anything except for the GPUs. It seems like a colleague of ours is 
unhappy with the performance of his Xeon-based workstation and we might 
commandeer it to ease his pain.


Alex


On 10/3/2017 7:05 AM, Szilárd Páll wrote:

Hi,

I think the 1070s and 1080s are the best value for money. These days, given
that it's I think it costs ~20% more, the 1080 is probably a bit better
value for money, but it's going to be a bit above $500, I think.

Also note that we're working on new GPU acceleration-related features that
will change the CPU-GPU balance in many use-cases, so if you are planning
to buy hardware, you might want to give the new code (in still CR) a try.

Cheers,
--
Szilárd

On Tue, Oct 3, 2017 at 12:18 AM, Alex  wrote:


Hi all,

A quick question, likely for Szilárd...

Now that we got the taste of very decent GPU acceleration with Titan XP
cards, I might be getting a brand new workstation with a 22-core Xeon
without any GPUs. We plan to install two GPUs in there and Titan XPs would
be too expensive for us in this case.

Any suggestions on what to invest in for the sub-$500 range per card?

Thank you,

Alex
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 162, Issue 9

[ABEL Stephane]

Hi, 

In addition to my previous email

If you have all the parameters obtained from RESP and tleap program (mol2, 
frcmod and lib) you could use the ACPYPE program to obtain the itp file for 
GROMACS 

See  
http://www.shourjya.thinkbiosolution.com/assigning-point-charges-to-non-standard-molecules-for-md-simulation/

and http://webapps.ccpn.ac.uk/acpype/

Good luck


Stéphane Abel, Ph.D.

CEA Saclay DSV/ISVFJ/SB2SM
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60


--

Message: 3
Date: Tue, 3 Oct 2017 19:25:48 +0200 (CEST)
From: Sergio Manzetti 
To: gmx-users 
Subject: [gmx-users] Tutorial
Message-ID:
<1499903584.16707185.1507051548537.javamail.zim...@fjordforsk.no>
Content-Type: text/plain; charset=utf-8

Hi, is there a tutorial for importing fully charged non-peptid topologies for 
the AMBER FF ISBN type to GMX somewhere ?
Thanks

Sergio Manzetti

Fjordforsk AS
Midtun
6894 VangsnesNorge
Org.nr. 911 659 654
Tlf: +47 57695621?kolab  |  Nanofactory  |  AQ-Lab  |  FAP

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Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Because in tuturial , energygroups = protein JZ4So I think ,I 
have to seperate my ligand and Protein in .mdp files and determine H bonds? 


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 8:56 PM, Justin Lemkul  wrote:



On 10/3/17 1:08 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  So how should I split protein and ligand from each other to 
>create  .mdp files?
> 

I think you need to back up and explain in greater detail what you're trying to 
do. We were talking about pdb2gmx, which uses TER or chain identifiers in a PDB 
file to determine chains for writing topologies. Then we moved on to index 
files 
and now .mdp files? I'm lost, and it's very hard to provide help.

If you have a protein-peptide complex, you don't need any kind of special index 
groups for .mdp files or (likely) much else. The peptide ligand is still part 
of 
the "Protein" default group (you don't have to create it) and that works fine 
for a lot of things you might need to set up, like tc-grps.

-Justin

> 
> Sent from Yahoo Mail for iPhone
> 
> 
> On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 10/3/17 11:13 AM, farial tavakoli wrote:
>>    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
>>
> 
> Index files aren't used with pdb2gmx. The splitting functions of make_ndx 
> break
> a chain down into its component residues. That's not at all what you want to 
> do.
> 
> -Justin
> 
>>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul  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 
>>> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪
>>> 
>>> *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
>>>
>>> jalem...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Oh I am sorry. Yes  I am trying to run md on my protein peptide 
complex. At first you advice me to use pdb2gmx to generate a topology for my 
complex and  I did. Then  according to the protein ligand complex tuturial in 
gromacs, I defined newbox and solvate After adding ions, I need to do energy 
minimization and use .mdp file which I should specify energygrouos , But my 
protein and ligand are not sepearate from each other. I just eant to know isnt 
there any problem if protein and ligand are merged and not separated?
Best regardsFarial 


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 8:56 PM, Justin Lemkul  wrote:



On 10/3/17 1:08 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  So how should I split protein and ligand from each other to 
>create  .mdp files?
> 

I think you need to back up and explain in greater detail what you're trying to 
do. We were talking about pdb2gmx, which uses TER or chain identifiers in a PDB 
file to determine chains for writing topologies. Then we moved on to index 
files 
and now .mdp files? I'm lost, and it's very hard to provide help.

If you have a protein-peptide complex, you don't need any kind of special index 
groups for .mdp files or (likely) much else. The peptide ligand is still part 
of 
the "Protein" default group (you don't have to create it) and that works fine 
for a lot of things you might need to set up, like tc-grps.

-Justin

> 
> Sent from Yahoo Mail for iPhone
> 
> 
> On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 10/3/17 11:13 AM, farial tavakoli wrote:
>>    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
>>
> 
> Index files aren't used with pdb2gmx. The splitting functions of make_ndx 
> break
> a chain down into its component residues. That's not at all what you want to 
> do.
> 
> -Justin
> 
>>
>> Sent from Yahoo Mail for iPhone
>>
>>
>> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul  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 
>>> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪
>>> 
>>> *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
>>>
>>> jalem...@vt.edu  | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>>
>>

[gmx-users] Tutorial

[Sergio Manzetti]

Hi, is there a tutorial for importing fully charged non-peptid topologies for 
the AMBER FF ISBN type to GMX somewhere ?
Thanks

Sergio Manzetti

Fjordforsk AS
Midtun
6894 VangsnesNorge
Org.nr. 911 659 654
Tlf: +47 57695621Økolab  |  Nanofactory  |  AQ-Lab  |  FAP

-- 
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* 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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] peptide ligand

[Justin Lemkul]

On 10/3/17 1:08 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  So how should I split protein and ligand from each other to 
create  .mdp files?



I think you need to back up and explain in greater detail what you're trying to 
do. We were talking about pdb2gmx, which uses TER or chain identifiers in a PDB 
file to determine chains for writing topologies. Then we moved on to index files 
and now .mdp files? I'm lost, and it's very hard to provide help.


If you have a protein-peptide complex, you don't need any kind of special index 
groups for .mdp files or (likely) much else. The peptide ligand is still part of 
the "Protein" default group (you don't have to create it) and that works fine 
for a lot of things you might need to set up, like tc-grps.


-Justin



Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul  wrote:



On 10/3/17 11:13 AM, farial tavakoli wrote:

   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



Index files aren't used with pdb2gmx. The splitting functions of make_ndx break
a chain down into its component residues. That's not at all what you want to do.

-Justin



Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul  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 
*To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪

*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

jalem...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
--
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* 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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] peptide ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  So how should I split protein and ligand from each other to 
create  .mdp files?


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 7:59 PM, Justin Lemkul  wrote:



On 10/3/17 11:13 AM, farial tavakoli wrote:
>  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
> 

Index files aren't used with pdb2gmx. The splitting functions of make_ndx break 
a chain down into its component residues. That's not at all what you want to do.

-Justin

> 
> Sent from Yahoo Mail for iPhone
> 
> 
> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul  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 
>> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪
>> 
>> *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
>>
>> jalem...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 162, Issue 7

[zaved]

> 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 'help' to
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> 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. 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 +
> From: ABEL Stephane 
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>   
> Subject: [gmx-users] Charges and Antechamber
> Message-ID:
>   <3e39b768bb199548ab18f7289e7534af38818...@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 + (UTC)
> From: farial tavakoli 
> To: 
> Subject: Re: [gmx-users] peptide ligand
> Message-ID: <1201432437.876905.1507043638...@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 
> 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 
>> *To:* gmx-us...@gromacs.org; ?farial tavakoli? ?
>> 
>> *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
>>

Re: [gmx-users] checking simulation progress

[Tasneem Kausar]

see gmx check -h option

On 3 Oct 2017 21:33, "Bukunmi Akinwunmi"  wrote:

> 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
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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] checking simulation progress

[Justin Lemkul]

On 10/3/17 12:03 PM, Bukunmi Akinwunmi wrote:

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.



The -v option of mdrun prints a running estimate of time remaining, but if you 
didn't use it then it's no use to you during an ongoing run. Otherwise, just use 
tail on the .log file to see how far along things are.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] peptide ligand

[Justin Lemkul]

On 10/3/17 11:13 AM, farial tavakoli wrote:

  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



Index files aren't used with pdb2gmx. The splitting functions of make_ndx break 
a chain down into its component residues. That's not at all what you want to do.


-Justin



Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul  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 
*To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪

*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

jalem...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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[gmx-users] checking simulation progress

[Bukunmi Akinwunmi]

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
-- 
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Re: [gmx-users] Charges and Antechamber

[João Henriques]

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"  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
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Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

[Mark Abraham]

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  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
>
> jalem...@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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Re: [gmx-users] peptide ligand

[farial tavakoli]

 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


Sent from Yahoo Mail for iPhone


On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul  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 
> *To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪ 
> 
> *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
>
> jalem...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Charges and Antechamber

[ABEL Stephane]

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 
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Re: [gmx-users] Charges and Antechamber

[João Henriques]

This can potetially involve minimal editting or a lot of work. If you will
be using atom types already in place, you mainly need to edit the rtp file.
The charges, bonds and impropers go there. Other files need minimal work
like the residuetypes.dat and possibly the hdb, r2b, etc.

Avoid touching the original FF under share/gromacs/top. Make a copy of it
on your work directory and edit that one. Also, please don't take this task
lightly. Modifying a FF requires a good understanding of the task at hand.
Mistakes might become costly and may even go unnoticed while produce
wrong/false results.

João

On Oct 3, 2017 4:36 PM, "Sergio Manzetti" 
wrote:
>
> Thanks, in which file do you add your residue, do you have an example?
>
> Thanks!
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
|   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/
| FAP ]
>
>
>
> From: "João Henriques" 
> To: "gmx-users" 
> Sent: Tuesday, October 3, 2017 4:33:55 PM
> Subject: Re: [gmx-users] Charges and Antechamber
>
> I just left work and I'm terrible with typing on the phone, so please bear
> with me.
>
> Since I mostly work with proteins and modified residues it was always
worth
> it for me to edit the actual FF instead of making an itp by hand. This way
> I let pdb2gmx do the tedious work of building the topology for myself. I
> simply give it a structure and it does its magic. Is it less work?
Probably
> not, since editing a FF is not exactly the simplest of tasks and requires
a
> lot of attention and knowledge about what is where in the many files that
> come in a FF folder. Still, I find it to have more pros than cons.
>
> To summarize, I don't build the topology. I add my custom residue to the
FF
> and let pdb2gmx figure the rest out.
>
> Hope it made sense,
> Cheers,
> João
>
> On Oct 3, 2017 3:53 PM, "Sergio Manzetti" 
> wrote:
>
> Thanks Joao, I am on the way with the QM part, but making the topology for
> GMX is a little bit more complicated. I thought of generating one with
> ANTECHAMBER Of a neutral species, then edit the topology itp file
manually,
> but the propers are quite complex to re-edit.
>
> How did you get around this part?
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> | ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/
> | FAP ]
>
>
>
> From: "João Henriques" 
> To: "gmx-users" 
> Sent: Tuesday, October 3, 2017 3:50:55 PM
> Subject: Re: [gmx-users] Charges and Antechamber
>
> Hi!
>
> If your goal is to generate the atomic partial charges for a new
> residue/molecule (not existing in the FF you are interested in using),
then
> doing the QM calculations is a must in most cases. For example, AMBER FFs
> have a well documented and specific recipe you can easily follow, which
> involves deriving the electrostatic potential from QM calculations at a
> specific level of theory + basis sets and then using the RESP fit
procedure.
>
> Cornell, Wendy D., et al. "A second generation force field for the
> simulation of proteins, nucleic acids, and organic molecules." Journal of
> the American Chemical Society 117.19 (1995): 5179-5197.
>
> I've done this a couple of times and it was relatively simple. I never
> needed to use antechamber for anything else, all modelling and assignment
> of atom types were done manually. Exotic species might make things more
> complicated.
>
> P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For
> example, GROMOS FFs don't have a fixed recipe for obtaining the charges
> (you can even set them by hand according to your own whim), but the
> calculations must reproduce solvation enthalpies, etc. In sum, check the
> original literature on the FF you plan on using to understand how to
> calculate your own charges in a way that respects that specific FF's
> "philosophy".
>
> Hope it helps,
> João
>
>
>
> On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti <
> sergio.manze...@fjordforsk.no> wrote:
>
> > Hi, I was wondering what the best approach is to simulate a negatively
> > charged topology imported from ANTECHAMBER (which can't do integral
> > charges):
> >
> > 1. Do QM calculations on the molecule, then edit the output from
> > Antechamber
> >
> > or
> >
> > 2. Do something else.
> >
> > Sergio Manzetti
> >
> > [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
http://www.fjordforsk.no/
> > | ]
> > Midtun
> > 6894 Vangsnes
> > Norge
> > Org.nr. 911 659 654
> > Tlf: +47 57695621
> > [ http://www.oekola

Re: [gmx-users] Charges and Antechamber

[Sergio Manzetti]

Thanks, in which file do you add your residue, do you have an example? 

Thanks! 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "João Henriques"  
To: "gmx-users"  
Sent: Tuesday, October 3, 2017 4:33:55 PM 
Subject: Re: [gmx-users] Charges and Antechamber 

I just left work and I'm terrible with typing on the phone, so please bear 
with me. 

Since I mostly work with proteins and modified residues it was always worth 
it for me to edit the actual FF instead of making an itp by hand. This way 
I let pdb2gmx do the tedious work of building the topology for myself. I 
simply give it a structure and it does its magic. Is it less work? Probably 
not, since editing a FF is not exactly the simplest of tasks and requires a 
lot of attention and knowledge about what is where in the many files that 
come in a FF folder. Still, I find it to have more pros than cons. 

To summarize, I don't build the topology. I add my custom residue to the FF 
and let pdb2gmx figure the rest out. 

Hope it made sense, 
Cheers, 
João 

On Oct 3, 2017 3:53 PM, "Sergio Manzetti"  
wrote: 

Thanks Joao, I am on the way with the QM part, but making the topology for 
GMX is a little bit more complicated. I thought of generating one with 
ANTECHAMBER Of a neutral species, then edit the topology itp file manually, 
but the propers are quite complex to re-edit. 

How did you get around this part? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
| ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ 
| FAP ] 



From: "João Henriques"  
To: "gmx-users"  
Sent: Tuesday, October 3, 2017 3:50:55 PM 
Subject: Re: [gmx-users] Charges and Antechamber 

Hi! 

If your goal is to generate the atomic partial charges for a new 
residue/molecule (not existing in the FF you are interested in using), then 
doing the QM calculations is a must in most cases. For example, AMBER FFs 
have a well documented and specific recipe you can easily follow, which 
involves deriving the electrostatic potential from QM calculations at a 
specific level of theory + basis sets and then using the RESP fit procedure. 

Cornell, Wendy D., et al. "A second generation force field for the 
simulation of proteins, nucleic acids, and organic molecules." Journal of 
the American Chemical Society 117.19 (1995): 5179-5197. 

I've done this a couple of times and it was relatively simple. I never 
needed to use antechamber for anything else, all modelling and assignment 
of atom types were done manually. Exotic species might make things more 
complicated. 

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For 
example, GROMOS FFs don't have a fixed recipe for obtaining the charges 
(you can even set them by hand according to your own whim), but the 
calculations must reproduce solvation enthalpies, etc. In sum, check the 
original literature on the FF you plan on using to understand how to 
calculate your own charges in a way that respects that specific FF's 
"philosophy". 

Hope it helps, 
João 



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti < 
sergio.manze...@fjordforsk.no> wrote: 

> Hi, I was wondering what the best approach is to simulate a negatively 
> charged topology imported from ANTECHAMBER (which can't do integral 
> charges): 
> 
> 1. Do QM calculations on the molecule, then edit the output from 
> Antechamber 
> 
> or 
> 
> 2. Do something else. 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
> -- 
> 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-requ...@gromacs.org. 
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https://maillis

Re: [gmx-users] Charges and Antechamber

[João Henriques]

I just left work and I'm terrible with typing on the phone, so please bear
with me.

Since I mostly work with proteins and modified residues it was always worth
it for me to edit the actual FF instead of making an itp by hand. This way
I let pdb2gmx do the tedious work of building the topology for myself. I
simply give it a structure and it does its magic. Is it less work? Probably
not, since editing a FF is not exactly the simplest of tasks and requires a
lot of attention and knowledge about what is where in the many files that
come in a FF folder. Still, I find it to have more pros than cons.

To summarize, I don't build the topology. I add my custom residue to the FF
and let pdb2gmx figure the rest out.

Hope it made sense,
Cheers,
João

On Oct 3, 2017 3:53 PM, "Sergio Manzetti" 
wrote:

Thanks Joao, I am on the way with the QM part, but making the topology for
GMX is a little bit more complicated. I thought of generating one with
ANTECHAMBER Of a neutral species, then edit the topology itp file manually,
but the propers are quite complex to re-edit.

How did you get around this part?


Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
|   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/
| FAP ]



From: "João Henriques" 
To: "gmx-users" 
Sent: Tuesday, October 3, 2017 3:50:55 PM
Subject: Re: [gmx-users] Charges and Antechamber

Hi!

If your goal is to generate the atomic partial charges for a new
residue/molecule (not existing in the FF you are interested in using), then
doing the QM calculations is a must in most cases. For example, AMBER FFs
have a well documented and specific recipe you can easily follow, which
involves deriving the electrostatic potential from QM calculations at a
specific level of theory + basis sets and then using the RESP fit procedure.

Cornell, Wendy D., et al. "A second generation force field for the
simulation of proteins, nucleic acids, and organic molecules." Journal of
the American Chemical Society 117.19 (1995): 5179-5197.

I've done this a couple of times and it was relatively simple. I never
needed to use antechamber for anything else, all modelling and assignment
of atom types were done manually. Exotic species might make things more
complicated.

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For
example, GROMOS FFs don't have a fixed recipe for obtaining the charges
(you can even set them by hand according to your own whim), but the
calculations must reproduce solvation enthalpies, etc. In sum, check the
original literature on the FF you plan on using to understand how to
calculate your own charges in a way that respects that specific FF's
"philosophy".

Hope it helps,
João



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti <
sergio.manze...@fjordforsk.no> wrote:

> Hi, I was wondering what the best approach is to simulate a negatively
> charged topology imported from ANTECHAMBER (which can't do integral
> charges):
>
> 1. Do QM calculations on the molecule, then edit the output from
> Antechamber
>
> or
>
> 2. Do something else.
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> | ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [
> http://www.phap.no/ | FAP ]
>
> --
> 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-requ...@gromacs.org.
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Re: [gmx-users] Charges and Antechamber

[Sergio Manzetti]

Thanks Joao, I am on the way with the QM part, but making the topology for GMX 
is a little bit more complicated. I thought of generating one with ANTECHAMBER 
Of a neutral species, then edit the topology itp file manually, but the propers 
are quite complex to re-edit. 

How did you get around this part? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "João Henriques"  
To: "gmx-users"  
Sent: Tuesday, October 3, 2017 3:50:55 PM 
Subject: Re: [gmx-users] Charges and Antechamber 

Hi! 

If your goal is to generate the atomic partial charges for a new 
residue/molecule (not existing in the FF you are interested in using), then 
doing the QM calculations is a must in most cases. For example, AMBER FFs 
have a well documented and specific recipe you can easily follow, which 
involves deriving the electrostatic potential from QM calculations at a 
specific level of theory + basis sets and then using the RESP fit procedure. 

Cornell, Wendy D., et al. "A second generation force field for the 
simulation of proteins, nucleic acids, and organic molecules." Journal of 
the American Chemical Society 117.19 (1995): 5179-5197. 

I've done this a couple of times and it was relatively simple. I never 
needed to use antechamber for anything else, all modelling and assignment 
of atom types were done manually. Exotic species might make things more 
complicated. 

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For 
example, GROMOS FFs don't have a fixed recipe for obtaining the charges 
(you can even set them by hand according to your own whim), but the 
calculations must reproduce solvation enthalpies, etc. In sum, check the 
original literature on the FF you plan on using to understand how to 
calculate your own charges in a way that respects that specific FF's 
"philosophy". 

Hope it helps, 
João 



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti < 
sergio.manze...@fjordforsk.no> wrote: 

> Hi, I was wondering what the best approach is to simulate a negatively 
> charged topology imported from ANTECHAMBER (which can't do integral 
> charges): 
> 
> 1. Do QM calculations on the molecule, then edit the output from 
> Antechamber 
> 
> or 
> 
> 2. Do something else. 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
> -- 
> 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-requ...@gromacs.org. 
-- 
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Re: [gmx-users] Charges and Antechamber

[João Henriques]

Hi!

If your goal is to generate the atomic partial charges for a new
residue/molecule (not existing in the FF you are interested in using), then
doing the QM calculations is a must in most cases. For example, AMBER FFs
have a well documented and specific recipe you can easily follow, which
involves deriving the electrostatic potential from QM calculations at a
specific level of theory + basis sets and then using the RESP fit procedure.

Cornell, Wendy D., et al. "A second generation force field for the
simulation of proteins, nucleic acids, and organic molecules." Journal of
the American Chemical Society 117.19 (1995): 5179-5197.

I've done this a couple of times and it was relatively simple. I never
needed to use antechamber for anything else, all modelling and assignment
of atom types were done manually. Exotic species might make things more
complicated.

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For
example, GROMOS FFs don't have a fixed recipe for obtaining the charges
(you can even set them by hand according to your own whim), but the
calculations must reproduce solvation enthalpies, etc. In sum, check the
original literature on the FF you plan on using to understand how to
calculate your own charges in a way that respects that specific FF's
"philosophy".

Hope it helps,
João



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti <
sergio.manze...@fjordforsk.no> wrote:

> Hi, I was wondering what the best approach is to simulate a negatively
> charged topology imported from ANTECHAMBER (which can't do integral
> charges):
>
> 1. Do QM calculations on the molecule, then edit the output from
> Antechamber
>
> or
>
> 2. Do something else.
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
> --
> 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-requ...@gromacs.org.
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Charges and Antechamber

[Sergio Manzetti]

Hi, I was wondering what the best approach is to simulate a negatively charged 
topology imported from ANTECHAMBER (which can't do integral charges): 

1. Do QM calculations on the molecule, then edit the output from Antechamber 

or 

2. Do something else. 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] peptide ligand

[Justin Lemkul]

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 
*To:* gmx-us...@gromacs.org; ‪farial tavakoli‬ ‪ 


*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

jalem...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] peptide ligand

[Justin Lemkul]

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

[Justin Lemkul]

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] lower-end GPUs

[Szilárd Páll]

Hi,

I think the 1070s and 1080s are the best value for money. These days, given
that it's I think it costs ~20% more, the 1080 is probably a bit better
value for money, but it's going to be a bit above $500, I think.

Also note that we're working on new GPU acceleration-related features that
will change the CPU-GPU balance in many use-cases, so if you are planning
to buy hardware, you might want to give the new code (in still CR) a try.

Cheers,
--
Szilárd

On Tue, Oct 3, 2017 at 12:18 AM, Alex  wrote:

> Hi all,
>
> A quick question, likely for Szilárd...
>
> Now that we got the taste of very decent GPU acceleration with Titan XP
> cards, I might be getting a brand new workstation with a 22-core Xeon
> without any GPUs. We plan to install two GPUs in there and Titan XPs would
> be too expensive for us in this case.
>
> Any suggestions on what to invest in for the sub-$500 range per card?
>
> Thank you,
>
> Alex
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[gmx-users] peptide ligand

[‪farial tavakoli‬ ‪]

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. 
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


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