ff14SB. Does it matter for TiMerge?
I’ve since been able to use TiMerge successfully, for other systems, by specifying the tolerance and making sure all the waters/ions come after the before and after copies of the protein.
Best
Matthew
> On Aug 25, 2022, at 6:06 PM, Josiah Bones <Josiah.Bones.anu.edu.au> wrote:
>
>
> *Message sent from a system outside of UConn.*
>
>
> Are you using ff19SB?
> From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
> Sent: Friday, August 19, 2022 12:40:58 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] TiMerge doesn't work, or what am I doing wrong?
>
> Dear Amber Community,
>
> Following the lysozyme tutorial on thermodynamic integration for mutating a sidechain, TiMerge in ParmEd does not work if I issue
>
> tiMerge :1-162 :163-324 :99&!.1563,1564,1565,1566,1571,1572 :261&!.4166,4167,4168,4169,4174,4175
>
> Where copy #1 of the protein is :1-162, copy #2 is 163-324, and the softcore regions are :99 and :261, but excluding the backbone atoms of each.
>
> The error message is: TiMergeError: The number of nonsoftcore atoms in mol1mask and mol2mask must be the same.
>
> But that is simply not true. Only the sidechains of :99 and :261 change and that is what the above masks select. The total number of atoms for the non-softcore regions is 2603 in both cases.
>
> I really need help with this issue. Otherwise, I’m going to have to abandon using Amber for my next research endeavors, and I don’t want to have to do that.
>
> Tutorial referenced above: https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial9%2Findex.html%23sidechain_mini&data=05%7C01%7Cjosiah.bones%40anu.edu.au%7C4d1df081cffa44cdab4b08da812808c8%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637964306201882189%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=V2Ovsp4%2FLeBRddF6g4l5TFSCHqhF%2B8UyX0rt5oa08m0%3D&reserved=0 <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial9%2Findex.html%23sidechain_mini&data=05%7C01%7C%7C3772ff3186be4ac4276d08da86e61705%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637970620043217852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=012NXD7pnBruX78tp2hAojpWMoaX1EvbYWI8gmPuSKA%3D&reserved=0> <https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial9%2Findex.html%23sidechain_mini&data=05%7C01%7Cjosiah.bones%40anu.edu.au%7C4d1df081cffa44cdab4b08da812808c8%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637964306201882189%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=V2Ovsp4%2FLeBRddF6g4l5TFSCHqhF%2B8UyX0rt5oa08m0%3D&reserved=0 <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial9%2Findex.html%23sidechain_mini&data=05%7C01%7C%7C3772ff3186be4ac4276d08da86e61705%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637970620043217852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=012NXD7pnBruX78tp2hAojpWMoaX1EvbYWI8gmPuSKA%3D&reserved=0>>
>
> Best,
> Matthew
>
>
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Received on Thu Aug 25 2022 - 17:30:03 PDT
