Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

2018-02-15 Thread Easton J . W . 
Hi Justin,


That makes sense, I've found where the parameters are


Thanks for your help


James


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 14 February 2018 22:31:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology 
to gromacs



On 2/14/18 5:28 PM, Easton J.W. wrote:
> Hi Justin,
>
> Many thanks for the detailed reply.
>
> I just wanted to check that it doesn't matter that the A2C and A3C are not 
> present in the bonded and non-bonded itp files for the forcefield? Should 
> this not have given an error?

The topology snippet you showed an [atomtypes] directive with those
types defined, so they were in fact in the nonbonded parameter list by
virtue of being added just above the first [moleculetype], as is
permitted in GROMACS topologies. If there were missing parameters,
grompp would have failed with a fatal error, so presumably you also
included the necessary bonded parameters somewhere, too.

-Justin

> Kind regards,
>
> James
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: 14 February 2018 14:43:35
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Potential issue using acpype to convert amber 
> topology to gromacs
>
>
>
> On 2/14/18 9:42 AM, Justin Lemkul wrote:
>>
>> On 2/14/18 9:33 AM, Easton J.W. wrote:
>>> Thanks Justin,
>>>
>>>
>>> Will this effect the interactions (both bonded and non-bonded) that
>>> these atoms have, as their atom types are not in the forcefield itp
>>> files?
>> Missing atom types would cause grompp to fail; you'd never get to the
>> point where a simulation would be affected.
>>
>> You're introducing custom atom types in the topology itself, and
>> that's always legal before any [moleculetype] appears. The LJ
>> parameters come from the [atomtypes] directive. Masses and charges
>> present in that directive aren't used.
>>
> Actually, to clarify: *if* masses are present in the [atoms] directive
> of a [moleculetype], then the masses found in [atomtypes] are not used.
> Strictly speaking, it is not necessary to have explicit masses in
> [atoms], though nearly all topologies do.
>
> -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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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

2018-02-14 Thread Easton J . W . 
Hi Justin,

Many thanks for the detailed reply.

I just wanted to check that it doesn't matter that the A2C and A3C are not 
present in the bonded and non-bonded itp files for the forcefield? Should this 
not have given an error?

Kind regards,

James

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 14 February 2018 14:43:35
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology 
to gromacs



On 2/14/18 9:42 AM, Justin Lemkul wrote:
>
>
> On 2/14/18 9:33 AM, Easton J.W. wrote:
>> Thanks Justin,
>>
>>
>> Will this effect the interactions (both bonded and non-bonded) that
>> these atoms have, as their atom types are not in the forcefield itp
>> files?
>
> Missing atom types would cause grompp to fail; you'd never get to the
> point where a simulation would be affected.
>
> You're introducing custom atom types in the topology itself, and
> that's always legal before any [moleculetype] appears. The LJ
> parameters come from the [atomtypes] directive. Masses and charges
> present in that directive aren't used.
>

Actually, to clarify: *if* masses are present in the [atoms] directive
of a [moleculetype], then the masses found in [atomtypes] are not used.
Strictly speaking, it is not necessary to have explicit masses in
[atoms], though nearly all topologies do.

-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] Potential issue using acpype to convert amber topology to gromacs

2018-02-14 Thread Easton J . W . 
Thanks Justin,


Will this effect the interactions (both bonded and non-bonded) that these atoms 
have, as their atom types are not in the forcefield itp files?


Kind regards,


James


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 14 February 2018 14:22:11
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology 
to gromacs



On 2/14/18 7:14 AM, Easton J.W. wrote:
> Hi,
>
>
> I've used acpype to convert my prmtop and inpcrd files into gromacs format. 
> I'm using the amber14sb forcefield.
>
>
> At the top of the top file generated, is an [atomtypes] section. Most of the 
> atoms in this section were present in the atomtypes.atp and ffnonbonded.itp 
> so I deleted them however there were two atomtypes A2C and A3C that were not, 
> so I left them.
>
>
> Looking back at my files after running some simulations I have realised that 
> these were meant to be the 2C and 3C atomtypes, which had been converted. 
> I've also realised that they do not have any mass in the atomtypes section.
>
>
> ---
>
>
> [ atomtypes ]
> ;name   bond_type mass charge   ptype   sigma epsilon   
> Amb
>   A2C  A2C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
> 1.91  0.1094
>   A3C  A3C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
> 1.91  0.1094
>
> [ moleculetype ]
> ;namenrexcl
> Peptide   3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
> bond_type
>   1N 1   CYS N1-0.415700 14.01000 ; qtot -0.416
>   2H 1   CYS H2 0.271900  1.00800 ; qtot -0.144
>   3   CX 1   CYSCA3 0.021300 12.01000 ; qtot -0.123
>   4   H1 1   CYSHA4 0.112400  1.00800 ; qtot -0.010
>   5  A2C 1   CYSCB5-0.123100 12.01000 ; qtot -0.133
>   6   H1 1   CYS   HB26 0.111200  1.00800 ; qtot -0.022
>   7   H1 1   CYS   HB37 0.111200  1.00800 ; qtot 0.089
>   8   SH 1   CYSSG8-0.311900 32.06000 ; qtot -0.223
>   9   HS 1   CYSHG9 0.193300  1.00800 ; qtot -0.029
>  10C 1   CYS C   10 0.597301 12.01000 ; qtot 0.568
>  11O 1   CYS O   11-0.567901 16.0 ; qtot -0.000
>
> ---
>
> What will this mean for the simulations that I have run?

The mass and charge information will be taken from [atoms], which always
over-writes [atomtypes] for those quantities. So there should be no
physical problem, e.g. from a "massless" atom. You can verify the masses
by using gmx dump on your .tpr file and checking that they're non-zero
for those atoms, but grompp would have failed before that point if they
were truly massless.

-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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[gmx-users] Potential issue using acpype to convert amber topology to gromacs

2018-02-14 Thread Easton J . W . 
Hi,


I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm 
using the amber14sb forcefield.


At the top of the top file generated, is an [atomtypes] section. Most of the 
atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so 
I deleted them however there were two atomtypes A2C and A3C that were not, so I 
left them.


Looking back at my files after running some simulations I have realised that 
these were meant to be the 2C and 3C atomtypes, which had been converted. I've 
also realised that they do not have any mass in the atomtypes section.


---


[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 A2C  A2C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094
 A3C  A3C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094

[ moleculetype ]
;namenrexcl
Peptide   3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
 1N 1   CYS N1-0.415700 14.01000 ; qtot -0.416
 2H 1   CYS H2 0.271900  1.00800 ; qtot -0.144
 3   CX 1   CYSCA3 0.021300 12.01000 ; qtot -0.123
 4   H1 1   CYSHA4 0.112400  1.00800 ; qtot -0.010
 5  A2C 1   CYSCB5-0.123100 12.01000 ; qtot -0.133
 6   H1 1   CYS   HB26 0.111200  1.00800 ; qtot -0.022
 7   H1 1   CYS   HB37 0.111200  1.00800 ; qtot 0.089
 8   SH 1   CYSSG8-0.311900 32.06000 ; qtot -0.223
 9   HS 1   CYSHG9 0.193300  1.00800 ; qtot -0.029
10C 1   CYS C   10 0.597301 12.01000 ; qtot 0.568
11O 1   CYS O   11-0.567901 16.0 ; qtot -0.000

---

What will this mean for the simulations that I have run?


Kind regards,


James
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Re: [gmx-users] Creating cyclic peptides

2017-10-17 Thread Easton J . W . 
Dear Maud,


Thanks, I will give that a try,


Regards,


James


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Maud Jusot 

Sent: 17 October 2017 16:10:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Creating cyclic peptides

Dear James,

If you want to use an Amber force field, you can create the topology in
the amber format with AmberTool and then convert it to the gromacs
format using Acpype tool
(http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder). It works for
cyclic peptides.

Best regards,

Maud

Le 17/10/2017 à 16:54, Easton J.W. a écrit :
> Thanks Justin,
>
>
> Is there anyway of getting it to work using an AMBER forcefield as well?
>
>
> Kind regards,
>
>
> James
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: 17 October 2017 15:46:27
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Creating cyclic peptides
>
>
>
> On 10/17/17 10:13 AM, Easton J.W. wrote:
>> Hi,
>>
>>
>> I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able 
>> to do this using either an AMBER or CHARMM forcefield.
>>
>>
>> Initially I have been following the instructions in this link,
>>
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html
>>
>>
>> However this will not work using an AMBER forcefield... I've attempted to 
>> search for an answer to this but I haven't been able to find anything. I 
>> have seen a few mentions of using "specbond.dat", however very few details 
>> on how to do this.
>>
>>
>> I'm fairly new to using GROMACS and so any help or advice that you can give 
>> would be appreciated
>>
> pdb2gmx doesn't like to deal with cyclic peptides. You can probably make
> it work but the easier approach (if you want to use the CHARMM force
> field) is to build the topology with the online CHARMM-GUI server.
>
> -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
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Re: [gmx-users] Creating cyclic peptides

2017-10-17 Thread Easton J . W . 
Thanks Justin,


Is there anyway of getting it to work using an AMBER forcefield as well?


Kind regards,


James


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 17 October 2017 15:46:27
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Creating cyclic peptides



On 10/17/17 10:13 AM, Easton J.W. wrote:
> Hi,
>
>
> I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to 
> do this using either an AMBER or CHARMM forcefield.
>
>
> Initially I have been following the instructions in this link,
>
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html
>
>
> However this will not work using an AMBER forcefield... I've attempted to 
> search for an answer to this but I haven't been able to find anything. I have 
> seen a few mentions of using "specbond.dat", however very few details on how 
> to do this.
>
>
> I'm fairly new to using GROMACS and so any help or advice that you can give 
> would be appreciated
>

pdb2gmx doesn't like to deal with cyclic peptides. You can probably make
it work but the easier approach (if you want to use the CHARMM force
field) is to build the topology with the online CHARMM-GUI server.

-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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[gmx-users] Creating cyclic peptides

2017-10-17 Thread Easton J . W . 
Hi,


I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to 
do this using either an AMBER or CHARMM forcefield.


Initially I have been following the instructions in this link,


https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html


However this will not work using an AMBER forcefield... I've attempted to 
search for an answer to this but I haven't been able to find anything. I have 
seen a few mentions of using "specbond.dat", however very few details on how to 
do this.


I'm fairly new to using GROMACS and so any help or advice that you can give 
would be appreciated


Kind regards,


James Easton
PhD Student, Tavassoli Group, Essex Group
School of Chemistry, University of Southampton

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