Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 118

[niki24]

>
> On 5/31/18 10:54 AM, nik...@tezu.ernet.in wrote:
>> Hello,
>>
>> Can anyone provide me with the correct topolgy file for
>> Adenosine-5'-Monophosphate(AMP).
>
> AMP is part of the CHARMM36 force field. Generate the topology with
> pdb2gmx.
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>
> -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.thelemkullab.com
>
> ==
>
>
>
> --
> Dear Justin,

Thanks a lot for your reply.
I have generated the topology using CHARMM36 forcefield.
But, however i would like to convert it into an itp file to
be used in gromos54a7 force field.

I am not being able to properly generate the itp file.

I have attached the topol.top file generated for AMP through CHARMM36 in
the link provided.

https://www.dropbox.com/s/uetrnnim4a30j01/topol.top?dl=0

Thanks


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[gmx-users] AMP_itp

[niki24]

Hello,

Can anyone provide me with the correct topolgy file for
Adenosine-5'-Monophosphate(AMP).

Thanks
Nikita Bora


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[gmx-users] (no subject)

[niki24]

Hello,

Can anyone provide me the topology for Adenosine Monophosphate Molecule
(AMP)for  Gromacs (gromos54a7 forcefield).

Thanks
Nikita Bora


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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 96

[niki24]

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> Today's Topics:
>
>1. topology file (mostafa paknia)
>2. Re: topology file (Soham Sarkar)
>3. Re: topology file (Justin Lemkul)
>4. Regarding calculation of SDF (Dilip.H.N)
>5. Re: gromacs.org_gmx-users Digest, Vol 169, Issue 89
>   (nik...@tezu.ernet.in)
>
>
> --
>
> Message: 1
> Date: Sun, 27 May 2018 23:00:26 +0330
> From: mostafa paknia 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] topology file
> Message-ID:
>   

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 89

[niki24]

> Message: 1
> Date: Thu, 24 May 2018 17:31:00 +0530
> From: nik...@tezu.ernet.in
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] AMP_simulation
> Message-ID:
>   <6be73c5ff3ffc470d178638a18b6e33f.squir...@webmail.tezu.ernet.in>
> Content-Type: text/plain;charset=utf-8
>
> Hello,
>
> I have tried doing the Molecular dynamics simulation of AMP using the
> Gromos54a7 forcefield.
>
> ITP parameters for the AMP molecule has been generated using the ATB
> builder. Minimization of the molecule goes on well however while carrying
> out the Nvt theres a segmantation fault resulting in step files.
>
> Moreover LINCS warning are shown with bonds that rotated more than 30
> degrees. ihave tried changing lincs parameter and also increasing the step
> size, but still simulation crashes.
>
> Is it suggestible to generate topology for the AMP molecule from the
> available topological parameters of ATP in GROMACS. Or are their any
> source of getting the correct itp paremeters for "AMP".
>
> Thanks
> Nikita Bora
>
>

>
> Message: 2
> Date: Thu, 24 May 2018 18:38:53 +0530
> From: Soham Sarkar 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] AMP_simulation
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
>
> Try with 1ps time step
>
> On Thu, 24 May 2018, 6:33 pm ,  wrote:
>
>> Hello,
>>
>> I have tried doing the Molecular dynamics simulation of AMP using the
>> Gromos54a7 forcefield.
>>
>> ITP parameters for the AMP molecule has been generated using the ATB
>> builder. Minimization of the molecule goes on well however while
>> carrying
>> out the Nvt theres a segmantation fault resulting in step files.
>>
>> Moreover LINCS warning are shown with bonds that rotated more than 30
>> degrees. ihave tried changing lincs parameter and also increasing the
>> step
>> size, but still simulation crashes.
>>
>> Is it suggestible to generate topology for the AMP molecule from the
>> available topological parameters of ATP in GROMACS. Or are their any
>> source of getting the correct itp paremeters for "AMP".
>>
>> Thanks
>> Nikita Bora
>>
>>
>>
>
> Message: 3
> Date: Thu, 24 May 2018 18:43:01 +0530
> From: RAHUL SURESH 
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] AMP_simulation
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
>
> Hi
>
> On Thu, May 24, 2018 at 5:31 PM,  wrote:
>
>> Hello,
>>
>> I have tried doing the Molecular dynamics simulation of AMP using the
>> Gromos54a7 forcefield.
>>
>> ITP parameters for the AMP molecule has been generated using the ATB
>> builder. Minimization of the molecule goes on well however while
>> carrying
>> out the Nvt theres a segmantation fault resulting in step files.
>>
>
> Segmentation fault normally occurs for large system with small memory.
> You
> can write xtc which is a compresssed trajectory file.
> Adding time steps to write the file.
>
>>
>> Moreover LINCS warning are shown with bonds that rotated more than 30
>> degrees. ihave tried changing lincs parameter and also increasing the
>> step
>> size, but still simulation crashes.
>>
>
> Lincs warning, as for here without knowing exactly about the system, i
> think the error is due to improper minimization.
> Minimize properly ir go for double precision method.
>
>>
>> Is it suggestible to generate topology for the AMP molecule from the
>> available topological parameters of ATP in GROMACS. Or are their any
>> source of getting the correct itp paremeters for "AMP".
>>
>
> Yeah, not an issue I guess.
>
>>
>> Thanks
>> Nikita Bora
>>
>
> Thanks back
>
-
> *Regards,*
> *Rahul *
>
>
> --
>
> Message: 4
> Date: Thu, 24 May 2018 18:43:01 +0530
> From: RAHUL SURESH 
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] AMP_simulation
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
>
> Hi
>
> On Thu, May 24, 2018 at 5:31 PM,  wrote:
>
>> Hello,
>>
>> I have tried doing the Molecular dynamics simulation of AMP using the
>> Gromos54a7 forcefield.
>>
>> ITP parameters for the AMP molecule has been generated using the ATB
>> builder. Minimization of the molecule goes on well however while
>> carrying
>> out the Nvt theres a segmantation fault resulting in step files.
>>
>
> Segmentation fault normally occurs for large system with small memory.
> You
> can write xtc which is a compresssed trajectory file.
> Adding time steps to write the file.
>
>>
>> Moreover LINCS warning are shown with bonds that rotated more than 30
>> degrees. ihave tried changing lincs parameter and also increasing the
>> 

[gmx-users] AMP_simulation

[niki24]

Hello,

I have tried doing the Molecular dynamics simulation of AMP using the
Gromos54a7 forcefield.

ITP parameters for the AMP molecule has been generated using the ATB
builder. Minimization of the molecule goes on well however while carrying
out the Nvt theres a segmantation fault resulting in step files.

Moreover LINCS warning are shown with bonds that rotated more than 30
degrees. ihave tried changing lincs parameter and also increasing the step
size, but still simulation crashes.

Is it suggestible to generate topology for the AMP molecule from the
available topological parameters of ATP in GROMACS. Or are their any
source of getting the correct itp paremeters for "AMP".

Thanks
Nikita Bora


* * * D I S C L A I M E R * * *
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disseminate, distribute or copy this e-mail. Please notify the sender 
immediately by e-mail if you have received this e-mail in error and destroy it 
from your system. Though considerable effort has been made to deliver error 
free e-mail messages but it can not be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, delayed, or may 
contain viruses. The recipient must verify the integrity of this e-mail message.
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Gromacs Users mailing list

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