Re: [AMBER] Joining two molecules

From: Gustaf Olsson <>
Date: Wed, 26 May 2021 07:49:31 +0000

Med vänlig hälsning
Gustaf Olsson
Gustaf Olsson, fil.dr

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On 25 May 2021, at 16:05, Dr. Anselm Horn <<>> wrote:

Hi Gustaf,

your general approach loading entities into leap, manually create bonds,
then (try to) save top/crd files seems ok (at least to me).

However, you have to ensure that you load/create molecular entities,
which still can be bonded together: Either you delete those atoms
manually, which were added by leap according to the unit description,
and then add the bond; or you update the actual unit description for
your molecular entities, so that no additional atoms are created by
tleap during loading and the two units just lack a single valence each -
which you then add.

We had faced a similar problem in the past, where we were interested in
carbohydrates with acyl substitutents. At that time we refrained from
mixing force field descriptions within a single molecule, and created
acyl-chain parameters 'in the spirit' of Glycam, essentially generating
isolated acyl residues (DOI: 10.1038/s41598-018-23624-8 -> supplement).

Thus, if intending to mix parameters in a molecule, I'd ensure that the
molecular fragments represent defined force field residues, for which
parameters already exist. The second step then was to come up with
parameters for the joint.

Best regards,


Friedrich-Alexander-Universität Erlangen-Nürnberg

On 05/25/2021 12:19 PM, Gustaf Olsson wrote:
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

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Received on Wed May 26 2021 - 01:00:02 PDT
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