[AMBER] substitution of fluorine atom at o9 hydroxyl group sialic acid by using glycam force field -reg

From: Jeyaram R A <ra.jeyaram.vit.ac.in>
Date: Mon, 10 Jun 2019 05:30:32 +0000

Dear Amber Users,


                        I want to substitute fluorine atom into any one hydroxyl group (o2, o4, o7, o8, o9 ) of sialic acid. I am able to substitute fluorine atom into any hydroxyl of sialic acid by using Generalized Amber force field (gaff). But I don't know, how to do is in glycam force field. During the substitution of fluorine atom into any hydroxyl of sialic acid, it shows the fatal error in tleap. In the following I attach the sialic acid pdb file with the substitution of fluorine atom at O9 hydroxyl of sialic acid. Can any one help me to solve this problem and tell me what are changes needed in my pdb file.

FATAL: Atom .R<0SA 387>.A<F9 38> does not have a type.

Thanks and regards

R. A. Jeyaram


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Received on Sun Jun 09 2019 - 23:00:02 PDT