multiple chain protein

[Christinele14]

I successfully prepared the amber topology for the complex 1A0Q (https://www.rcsb.org/structure/1A0Q). However, when I used acpype to generate the Gromacs topology, it seemed that two chains in my protein are merged into one. It seemed weird. So could you please take a look at it? Thank you.

[alanwilter]

If you only could show me the steps, in detail, that you did...

But I suspect you didn't cap your chains with N and C terminals while using tleap.

[Christinele14]

Yeap. Here is my tleap.in file. Yes, I guess I have to add the chain information inside tleap. Could you please take a look and suggest how could I add chain information inside so that two chains could be identified? Thank you in advance.

`source oldff/leaprc.ff99SB source leaprc.gaff2 source leaprc.water.tip3p

loadamberprep 1a0q_ligand_h_cleaned.prepi loadamberparams 1a0q_ligand_h_cleaned.frcmod mol = loadpdb cat_1a0q_complex.pdb

solvatebox mol TIP3PBOX 8 addions mol Cl- 0 saveamberparm mol 1a0q_complex.prmtop 1a0q_complex.inpcrd quit `

[alanwilter]

Have a look here https://github.com/alanwilter/acpype/wiki/Tutorial-NAMD

But your protein has problems. Have you seen its 3D? https://www.rcsb.org/3d-view/1A0Q

Have you read the PDB header?

REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     ASP L     1                                                      
REMARK 465     GLU H     1                                                      
REMARK 465     GLY H    98                                                      
REMARK 465     ARG H    99                                                      
REMARK 465     SER H   100                                                      
REMARK 465     ASN H   100A                                                     
REMARK 465     GLY H   127                                                      
REMARK 465     SER H   128                                                      
REMARK 465     ALA H   129                                                      
REMARK 465     ALA H   130                                                      
REMARK 465     GLN H   131                                                      
REMARK 465     THR H   132                                                      
REMARK 465     ASN H   133                                                      

tleap already does the terminals accordingly, but there are several things to pay attention. You likely need to learn tleap properly. But first you really need to know your protein and your input PDB.

I really doubt we have a ACPYPE issue here.