[AMBER] Joining two molecules

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Tue, 25 May 2021 10:19:30 +0000

I’ve been looking at the tutorials and some other material for a while now and I cannot figure out how I have ever managed to proceed past the step where structures are supposed to be joined.

I’m trying to use to different FFs for 2 parts of 1 larger molecule (gaff and glycam), the idea here was to align an NH2 group of a substituent with a OH group on a carbohydrate. I deleted the “overlapping” atoms leaving the two molecules reasonably oriented with a R-(C=O)-NH- -C gap. The plan is to connect/bond N-C and then use frcmod to adapt reasonable parameters for the “amide” group from glycam.

However, trying to keep the connect record, or renumbering the connect records in the joined file, breaks it. Fatal error in leap and refusing to open in any other application. in order to use the file I had to remove the connect records.

Now, I thought I’d be able to use leap to figure out what parameters for the N-C bond I need to add. Opening the joint PDB file with the prep/frcmod and glycam in leap, “missing atoms” are added from residue template(s). This is not really what I want to happen as I cannot “bond” the N-C atoms and I now have overlapping atoms. I also loose a ring C3-C4 bond in the carbohydrate when I remove the connect record.

Either I am missing some step of which I am unaware or I am approaching this in a completely flawed way. Can I load my joint PDB file, ignoring missing atoms in residue template and then joint them to form a molecule to figure out what parameters I am missing with leap, or should I investigate a different approach?

Best regards
// Gustaf

AMBER mailing list
Received on Tue May 25 2021 - 03:30:02 PDT
Custom Search