Re: [GaMD-discuss] error with amber24 GaMD-PPI Too many TI atoms--current limit: 500 atoms

[Miao, Y. <Yin...@me...>]

Hi Christian,

Sorry for the issue with running PPI-GaMD. To perhaps follow up with the post by Dr. Fabian Glaser as you mentioned in your email, I’m attaching more detailed discussion he had later on with Jinan to resolve the issue.

Hope the example “gti_controlVariable.i” and the idea of using “only the interfacial atoms of the first protein in TIMASK1/SCMASK1, and then the second FULL protein first and last atoms in bgpro2atm and edprod2atm” could help.

For “bgpro2atm and edpro2atm”, it would make sense to include ALL atoms associated with the second protein, including the PTMs.

Best,
Yinglong



Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology and
Computational Medicine Program
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org<http://miaolab.org/>

Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov

On Oct 29, 2025, at 5:03 PM, Christian Seitz <cgs...@gm...> wrote:

You don't often get email from cgs...@gm.... Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Hello Yinglong + co,

I am trying to equilibrate a system for use in GaMD-PPI using amber24. I ran it through normal equilibration for MD (heating, minimizing, equilibration) already. I tried to start a GaMD equilibration, but immediately the system fails with a segfault:

terminate called after throwing an instance of 'std::runtime_error'
  what():  Too many TI atoms--current limit: 500 atoms

I went into $AMBERHOME/amber/pmemd24_src/src/pmemd/src/gti_controlVariable.i and changed the following parameters:

MaxNumberTIAtom = 750 -> 5250
MaxNumberTIPair = 300 -> 3000
MaxNumberREAFAtom = 500 -> 4000

I can make a fresh build of amber24 and compile with these adjusted parameters, but running it still results in a TI atom limit of 500 atoms. This issue was seen previously here<http://archive.ambermd.org/202412/0029.html>, here<https://sourceforge.net/p/gamd/mailman/gamd-discuss/thread/SA1PR03MB6450A4FB3834171AE436C154B85F2%40SA1PR03MB6450.namprd03.prod.outlook.com/#msg58743189>, here<http://archive.ambermd.org/202206/0050.html>, and here<http://archive.ambermd.org/202307/0086.html>. It appears one person<https://sourceforge.net/p/gamd/mailman/gamd-discuss/thread/36223A2E-0AC1-4D6B-8F42-E1B5C996FE4F%40uconn.edu/> was able to fix this issue in a previous version of amber, but not amber24. Do you have any ideas on what other parameters I would need to modify to increase the TI atom limit? Thank you!

I also have a question about the atom masks. When I select the atom mask bgpro2atm and edpro2atm, should this mask only include protein atoms or also PTMs, such as glycans, attached to the protein?

Thanks for your help!

Best,
Christian

--
Christian Seitz
PhD, Biochemistry & Biophysics | UCSD
Postdoc, Computer Science | UChicago
cgs...@gm...<mailto:cg...@uc...>
[www.linkedin.com/in/christianseitz21]<http://www.linkedin.com/in/christianseitz21>
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