Re: [AMBER] How to make sure there is bond in my complex

From: Thakur, Abhishek <axt651.miami.edu>
Date: Thu, 20 Apr 2017 19:23:09 +0000

Yes I have got it by printbonds commands

________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, April 20, 2017 8:17:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make sure there is bond in my complex

I guess "bond" command. But please try playing with "help" in
interactive command first. It's much easier to "see" it.

Hai

On Thu, Apr 20, 2017 at 3:06 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi Hai
>
> Do you mean something like hydrogen bond analysis ?
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Thursday, April 20, 2017 7:59:20 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to make sure there is bond in my complex
>
> Hi, you can use cpptraj or ParmED interactive mode to print out the
> bond information. Use "help" or manual for info.
>
> Hai
>
> On Thu, Apr 20, 2017 at 2:56 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>> Hi everyone,
>>
>>
>> I have made a complex with tleap.
>>
>> In that complex I have made 6 bonds using bond command.
>>
>> But when I visualize that in chimera I am unable to find any bonds.
>>
>> So then I have used my prmtop and inpcrd file and cpptraj to generate pdb file for me to make sure there is a bond. But not I can see one of the bonds, remaining 5 bonds are not shown by chimera till now.
>>
>> Then I have visualized in VMD and I can find 5 bonds but still 1 bond is missing.
>>
>>
>> Can anyone suggest me a way by which I can make sure that my parameter files have bonds.
>>
>>
>>
>>
>> with regards,
>>
>> -Abhi
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=M6qNYcHxUz6xIWUt3dIb3j1aDAxLF2gGN_49GmnGr5Y&s=JvM3PVJZCo_4ByQjluBxzlbfjbxTo_x-oBY2a2oyCyg&e=
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=M6qNYcHxUz6xIWUt3dIb3j1aDAxLF2gGN_49GmnGr5Y&s=JvM3PVJZCo_4ByQjluBxzlbfjbxTo_x-oBY2a2oyCyg&e=
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=l9jvwv4A0vtmEpEJMGg4n4_0gHqkpB8M2hFUtSiFDoI&s=HrXd5Vp6epJG4ToJaLXEOYXYkl8SfgHKRDkam4BmE1g&e=

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=l9jvwv4A0vtmEpEJMGg4n4_0gHqkpB8M2hFUtSiFDoI&s=HrXd5Vp6epJG4ToJaLXEOYXYkl8SfgHKRDkam4BmE1g&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 20 2017 - 12:30:04 PDT
Custom Search