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
questions.
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
residues.
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
Chetna
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Received on Fri Mar 23 2018 - 04:00:02 PDT
