pren
commented
7 months ago Poltype2 default is not adding hydrogen to your input molecule, even though it generates the different states. Can you compare the opt input and your input molecule (sdf) to confirm?
From: blakemertz @.> Date: Tuesday, April 2, 2024 at 5:16 PM To: TinkerTools/poltype2 @.> Cc: Subscribed @.***> Subject: [TinkerTools/poltype2] selectivity of tautomers for parameterization (Issue #41)
Is there a way to guide poltype2 in choosing a subset of tautomers for small molecule parameterization? I have a small molecule with 4 tautomeric states, but upon visual inspection, State_1 and State_3 are incorrect based on my known chemistry. Here is what poltype2 has generated so far:
ls -ltr
total 736
-rwxr-xr-x 1 blake blake 48 Apr 2 15:04 poltype.ini
-rw-r--r-- 1 blake blake 5869 Apr 2 15:04 MDH-195.sdf
-rw-r--r-- 1 blake blake 5270 Apr 2 15:04 MDH-195.mol
-rw-r--r-- 1 blake blake 5270 Apr 2 15:05 conftest.mol
-rw-r--r-- 1 blake blake 5270 Apr 2 15:05 extendedconf.mol
-rw-r--r-- 1 blake blake 5869 Apr 2 15:05 IonizationState_0.sdf
-rw-r--r-- 1 blake blake 5270 Apr 2 15:05 IonizationState_0.mol
-rw-r--r-- 1 blake blake 5979 Apr 2 15:05 IonizationState_1.sdf
-rw-r--r-- 1 blake blake 5371 Apr 2 15:05 IonizationState_1.mol
-rw-r--r-- 1 blake blake 5869 Apr 2 15:05 TautomerState_0.sdf
-rw-r--r-- 1 blake blake 5270 Apr 2 15:05 TautomerState_0.mol
-rw-r--r-- 1 blake blake 5869 Apr 2 15:05 TautomerState_1.sdf
-rw-r--r-- 1 blake blake 5270 Apr 2 15:05 TautomerState_1.mol
-rw-r--r-- 1 blake blake 5869 Apr 2 15:05 TautomerState_2.sdf
-rw-r--r-- 1 blake blake 5270 Apr 2 15:05 TautomerState_2.mol
-rw-r--r-- 1 blake blake 5869 Apr 2 15:05 TautomerState_3.sdf
-rw-r--r-- 1 blake blake 5270 Apr 2 15:05 TautomerState_3.mol
-rw-r--r-- 1 blake blake 2746 Apr 2 15:05 MDH-195-opt_1_temp.com
-rw-r--r-- 1 blake blake 4317 Apr 2 15:05 MDH-195-opt_1.psi4
-rw-r--r-- 1 blake blake 2746 Apr 2 15:05 MDH-195-opt_1.com
-rw-r--r-- 1 blake blake 431 Apr 2 15:05 MDH-195-poltype.log
-rw-r--r-- 1 blake blake 587296 Apr 2 17:09 MDH-195-opt_1.log
-rw-r--r-- 1 blake blake 65 Apr 2 17:09 psi.136377.clean
Is there a way to flag poltype2 so that it will skip over parameterization of State_1 and State_3? Or can I simply delete/move the unwanted tautomers? Otherwise I will be wasting twice as many CPU cycles to carry out this parameterization. Thanks.
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blakemertz
Is there a way to guide poltype2 in choosing a subset of tautomers for small molecule parameterization? I have a small molecule with 4 tautomeric states, but upon visual inspection, State_1 and State_3 are incorrect based on my known chemistry. Here is what poltype2 has generated so far:
Is there a way to flag poltype2 so that it will skip over parameterization of State_1 and State_3? Or can I simply delete/move the unwanted tautomers? Otherwise I will be wasting twice as many CPU cycles to carry out this parameterization. Thanks.