Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
________________________________
From: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Sent: Sunday, 1 March, 2020, 11:02 PM
To: SHAUNAK BADANI
Subject: Re: [AMBER] Issue in drug parameter
Hi David,
Thanks for your reply. I used autoimage and the drug is properly surrounded by water molecules now. However, I am not able to clearly understand the reason behind this behaviour as I used iwrap=1 during my equilibration, under the assumption that this won't occur. Could you suggest a plausible explanation?
Thanks,
Shaunak Badani
IIIT Hyderabad
________________________________
From: SHAUNAK BADANI <shaunak.badani.research.iiit.ac.in>
Sent: Sunday, March 1, 2020 7:50 PM
To: Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
Cc: Krishnan m.krishnan <m.krishnan.iiit.ac.in>
Subject: Fwd: [AMBER] Issue in drug parameter
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, March 1, 2020 7:02:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue in drug parameter
On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?
Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 01 2020 - 10:30:02 PST
