[AMBER] Problems with creating prmtop file from Charmm-GUI generated membrane system

From: Chetna Tyagi <cheta231.gmail.com>
Date: Fri, 23 Mar 2018 11:55:00 +0100

Dear all,

I have been trying for quite a long time to create my peptide-membrane
system for simulations. The peptide has 3 engineered residues of different
kinds. During the prompt to upload parameter and topology files for
engineered residues, only one residue can be uploaded. If I try to combine
the .par and .rtf files for all residues and upload as one, it shows an
error. Somehow, the CHARMM forum blocked me from registering to ask

Secondly, I made an only-membrane system and everything went fine until I
load the pdb file in leap. It shows lot of errors. So, I converted the file
using charmmlipid2amber.py script to convert the file. Now, no errors while
loading the pdb but it can't form the prmtop file.

I rechecke dmany times, I load all libraries solvent.lib for TIP3 waters,
lipid14 force field, protein force field. the frcmod.ions library also. And
I still get errors like,

"*The file contained 15047 atoms not in residue templates*"....

And upon trying to save prmtop....For example,

"FATAL: Atom .R<Cl- 5421>.A<Cl- 1> does not have a type" even when the CLA
atoms from CHARMM has been converted to Cl-.

"FATAL: Atom .R<WAT 5375>.A<O 1> does not have a type."

I am following the lipid tutorial of Amber.

Interestingly, the files downloaded from Charmm-GUI in amber formats
includes .parm7 and .rst7 through which the sander simulation could run
fine. I would have used this way if Charmm-GUI could support my engineered

Is there a better way to approach this problem? I just need my peptide with
membrane (not even inserted).

Any advice is well appreciated.
Best wishes
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Received on Fri Mar 23 2018 - 04:00:02 PDT
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