If you can, get rid of the packages that are giving you trouble:
-DDISABLE_TOOLS="rism;pbsa"
________________________________
From: amber-request.ambermd.org <amber-request.ambermd.org>
Sent: Thursday, March 6, 2025 3:00 PM
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Subject: AMBER Digest, Vol 4648, Issue 1
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AMBER Mailing List Digest
Today's Topics:
1. Re: Compilation errors with CUDA 12.6
(RUBEN ANTONIO ROMO MANCILLAS)
2. Re: Compilation errors with CUDA 12.6 (jimkress_58.kressworks.org)
3. Atom names failed (Carlos)
----------------------------------------------------------------------
Message: 1
Date: Thu, 6 Mar 2025 03:23:12 +0000
From: RUBEN ANTONIO ROMO MANCILLAS <romtono.comunidad.unam.mx>
To: "jimkress_58.kressworks.org" <jimkress_58.kressworks.org>, 'AMBER
Mailing List' <amber.ambermd.org>
Subject: Re: [AMBER] Compilation errors with CUDA 12.6
Message-ID:
<SN6PR07MB4831D6AA6D1A2474CE55B3EEE0CA2.SN6PR07MB4831.namprd07.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Thank you for your kind response. Unfortunately, downgrading cuda is not an option because we need that version or newer versions of cuda for another software essential to work with.
Any ideas how to adapt the code to recent versions of cuda would be appreciated.
Cheers,
Dr. Antonio Romo-Mancillas
School of Chemistry
Autonomous University of Queretaro
P?gina web: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2Fdacsif_uaq&data=05%7C02%7Cpb777%40iqb.rutgers.edu%7C2dfe6e64937341c4d1d508dd5ce98004%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638768880150630787%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=I6zSkKaPEu8Asw2hUNQyxp872ujDBLkcVZ9qLcDVCc8%3D&reserved=0<https://bit.ly/dacsif_uaq>
-----Original Message-----
From: jimkress_58.kressworks.org <jimkress_58.kressworks.org>
Sent: mi?rcoles, 5 de marzo de 2025 12:45 p. m.
To: RUBEN ANTONIO ROMO MANCILLAS <romtono.comunidad.unam.mx>; 'AMBER Mailing List' <amber.ambermd.org>
Subject: RE: [AMBER] Compilation errors with CUDA 12.6
CUDA 12.6 isn't supported. Try CUDA 11.X or CUDA 12.2
Jim
James Kress Ph.D., President
The KressWorksR Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation "ENGINEERING THE CURE" C
(248) 573-5499
Learn More and Donate At:
Website: https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kressworks.org%2F&data=05%7C02%7Cpb777%40iqb.rutgers.edu%7C2dfe6e64937341c4d1d508dd5ce98004%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638768880150643545%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=vItVResjjUpVqmk843OlRZP3PRE%2FeLJPdQUy22Lz2Sc%3D&reserved=0<http://www.kressworks.org/>
Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.
-----Original Message-----
From: RUBEN ANTONIO ROMO MANCILLAS via AMBER <amber.ambermd.org>
Sent: Wednesday, March 5, 2025 12:57 PM
To: amber.ambermd.org
Subject: [AMBER] Compilation errors with CUDA 12.6
Greetings,
Recently, I have tried to compile Amber in Ubuntu-WSL with cuda 12.6. The serial and parallel versions were compiled without errors, only some warnings on the tests. But when I tried to compile for GPU, at compiling cuda_LinearSolvers.cu, the errors in the attached file prevent the compilation.
Any help will be greatly appreciated.
Cheers,
Dr. Antonio Romo-Mancillas
School of Chemistry
Autonomous University of Queretaro
------------------------------
Message: 2
Date: Wed, 5 Mar 2025 23:38:41 -0500
From: <jimkress_58.kressworks.org>
To: "'RUBEN ANTONIO ROMO MANCILLAS'" <romtono.comunidad.unam.mx>,
"'AMBER Mailing List'" <amber.ambermd.org>
Subject: Re: [AMBER] Compilation errors with CUDA 12.6
Message-ID: <01a301db8e51$a452da30$ecf88e90$.kressworks.org>
Content-Type: text/plain; charset="iso-8859-1"
You can install an appropriate CUDA version in a different directory and
then point to that as part of the cmake file for AMBER.
Jim
James Kress Ph.D., President
The KressWorks? Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
?ENGINEERING THE CURE? ?
(248) 573-5499
Learn More and Donate At:
Website: https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kressworks.org%2F&data=05%7C02%7Cpb777%40iqb.rutgers.edu%7C2dfe6e64937341c4d1d508dd5ce98004%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638768880150655851%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2Fq0%2FnNWpOyZZhjZHZgM%2ByYtJ9EKhvq93dc69brNQGjk%3D&reserved=0<http://www.kressworks.org/>
Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.
-----Original Message-----
From: RUBEN ANTONIO ROMO MANCILLAS <romtono.comunidad.unam.mx>
Sent: Wednesday, March 5, 2025 10:23 PM
To: jimkress_58.kressworks.org; 'AMBER Mailing List' <amber.ambermd.org>
Subject: RE: [AMBER] Compilation errors with CUDA 12.6
Thank you for your kind response. Unfortunately, downgrading cuda is not an
option because we need that version or newer versions of cuda for another
software essential to work with.
Any ideas how to adapt the code to recent versions of cuda would be
appreciated.
Cheers,
Dr. Antonio Romo-Mancillas
School of Chemistry
Autonomous University of Queretaro
P?gina web: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2Fdacsif_uaq&data=05%7C02%7Cpb777%40iqb.rutgers.edu%7C2dfe6e64937341c4d1d508dd5ce98004%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638768880150668900%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=70VMgTcYFs6TOadSKjS5goUp%2Bf6yaeJceY6aUtbAfIc%3D&reserved=0<https://bit.ly/dacsif_uaq>
-----Original Message-----
From: jimkress_58.kressworks.org <jimkress_58.kressworks.org>
Sent: mi?rcoles, 5 de marzo de 2025 12:45 p. m.
To: RUBEN ANTONIO ROMO MANCILLAS <romtono.comunidad.unam.mx>; 'AMBER Mailing
List' <amber.ambermd.org>
Subject: RE: [AMBER] Compilation errors with CUDA 12.6
CUDA 12.6 isn't supported. Try CUDA 11.X or CUDA 12.2
Jim
James Kress Ph.D., President
The KressWorksR Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation "ENGINEERING
THE CURE" C
(248) 573-5499
Learn More and Donate At:
Website: https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kressworks.org%2F&data=05%7C02%7Cpb777%40iqb.rutgers.edu%7C2dfe6e64937341c4d1d508dd5ce98004%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638768880150681823%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ujs7HmasyOfN0rgC%2FXAS4zAewaLzCf7XwTr15SUCCLI%3D&reserved=0<http://www.kressworks.org/>
Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.
-----Original Message-----
From: RUBEN ANTONIO ROMO MANCILLAS via AMBER <amber.ambermd.org>
Sent: Wednesday, March 5, 2025 12:57 PM
To: amber.ambermd.org
Subject: [AMBER] Compilation errors with CUDA 12.6
Greetings,
Recently, I have tried to compile Amber in Ubuntu-WSL with cuda 12.6. The
serial and parallel versions were compiled without errors, only some
warnings on the tests. But when I tried to compile for GPU, at compiling
cuda_LinearSolvers.cu, the errors in the attached file prevent the
compilation.
Any help will be greatly appreciated.
Cheers,
Dr. Antonio Romo-Mancillas
School of Chemistry
Autonomous University of Queretaro
------------------------------
Message: 3
Date: Thu, 6 Mar 2025 13:54:25 -0600
From: Carlos <carlos.rom.74he.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Atom names failed
Message-ID:
<CAA_maK3P4LnJJyPj4JysRCSUN+GgUpXa57fxMm-tWeCTNb9Zvg.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi Dear all
I am trying to obtain topology and coordinates files for a simulation.
The molecule is p-nitrophenyl-B-D-glucopyraanose. I got SDF file from
pubchem, obtained pdb format with avogadro, and for frcmod I used
antechamber/ parmck2. Until this step everything is Ok.
So I docked the p-nitrophenyl-B-D-glucopyranose to a molecule and save
coordinates, however, when I tried to obtain topology and coordinates files
for the complex, there is an advice and tleap can?t build them.
The advice is the next:
Error: Atom .R<UNL 1>.A<C9 19> has force field coordination 4
but only 3 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon (if running interactively).
Error: Atom .R<UNL 1>.A<C11 21> has force field coordination 4
but only 3 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon (if running interactively).
Segmentation fault (core dumped)
The p-nitrophenyl group has an aromatic ring, so I think there should be C'
carbons, but I don?t know why antechamber assign C9, C10,C11, C12 atom
names.
Can somebody help me?
I appreciate it. Thanks on advance
Regards
------------------------------
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