amber99SB-disp water parameters

[kgaalswyk]

Hello,

I'm trying to use the 99SB-disp in amber20. I've copied the files into their respective directories as instructed. I run tleap:

source leaprc.protein.ff99SBdisp
source leaprc.water.tip4pd_disp

and I am able to solvate with TIP4PDBOX. However when it comes to saving the parameter and coordinate files I get errors:

Error: For atom (.R<WAT 4401>.A<H2 3>) could not find vdW (or other) parameters for type (HW)

I downloaded the git several days before so I still have the parm99.dat file that was recently removed. When I compare this file to the parm99.dat in amber20/dat/leap/parm I notice that the amber20 version does not include parameters for HW and OW which are in the parm99.dat file that was included previously. If I have that parm99.dat file in my working directory, it works as expected.

Would an acceptable solution be to source leaprc.water.tip3p before sourcing the tip4pd_disp file?

Thank you,
Kari Gaalswyk

[paulrobustelli]

Hello, I'm not actually familiar with the amber implementaiton, which was just conduced by Olga Lebedenko ***@***.***) - cc'd here, who has been running this implementation. Perhaps she can help you with your question. Please cc' me on the response as well so I know for future inquires. Best, Paul

…

________________________________ From: Kari ***@***.***> Sent: Thursday, February 9, 2023 1:42 PM To: paulrobustelli/Force-Fields ***@***.***> Cc: Subscribed ***@***.***> Subject: [paulrobustelli/Force-Fields] amber99SB-disp water parameters (Issue #15) Hello, I'm trying to use the 99SB-disp in amber20. I've copied the files into their respective directories as instructed. I run tleap: source leaprc.protein.ff99SBdisp source leaprc.water.tip4pd_disp and I am able to solvate with TIP4PDBOX. However when it comes to saving the parameter and coordinate files I get errors: Error: For atom (.R<WAT 4401>.A<H2 3>) could not find vdW (or other) parameters for type (HW) I downloaded the git several days before so I still have the parm99.dat file that was recently removed. When I compare this file to the parm99.dat in amber20/dat/leap/parm I notice that the amber20 version does not include parameters for HW and OW which are in the parm99.dat file that was included previously. If I have that parm99.dat file in my working directory, it works as expected. Would an acceptable solution be to source leaprc.water.tip3p before sourcing the tip4pd_disp file? Thank you, Kari Gaalswyk — Reply to this email directly, view it on GitHub<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fpaulrobustelli%2FForce-Fields%2Fissues%2F15&data=05%7C01%7CPaul.J.Robustelli%40Dartmouth.edu%7Ccafbd9eed04d440b705708db0acd6987%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C638115649571908693%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lmJgIbfMEV2vRTI6rUBcfI80sACmCmW0nJ59bWWbG04%3D&reserved=0>, or unsubscribe<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAN3Z4TIQXFJISVXSGS4MOTLWWU3BVANCNFSM6AAAAAAUW44TUI&data=05%7C01%7CPaul.J.Robustelli%40Dartmouth.edu%7Ccafbd9eed04d440b705708db0acd6987%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C638115649571908693%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2BKyHdyf8gVBS8pIaGZZZUz6iuvvbBzwNfhVfuVbYDh0%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[OOLebedenko]

Hello,

Please, use the actual version frcmod.tip4pd_disp from the main branch.
I transfer HW parameters from old version parm99.dat to frcmod.tip4pd_disp
(see the corresponding commit)

The reason for the confusion is because the old version parm99.dat file contains TIP3P water parameters (removed from repo),
but the current version in AmberTools has taken those out (parm99.dat in amber20/dat/leap/parm) -- users must
specify a water force field, and there is no default.

Please, let me know if something goes wrong