# PMX Ligand Preparation from Scratch - Atom Types and Parameter Discrepancies

**URL:** <https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429>\
**Category:** pmx\
**Tags:** pmx, support, tutorials, community\
**Created:** [February 16, 2025, 3:24pm UTC](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429 "2025-02-16T15:24:36Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![jinurajkr](https://avatars.discourse-cdn.com/v4/letter/j/d26b3c/32.png) [@jinurajkr](https://ask.bioexcel.eu/u/jinurajkr)\
**Post date:** [February 16, 2025, 3:24pm UTC](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429/1 "2025-02-16T15:24:36Z")

</div>

Dear All

We are writing to you regarding the preparation of ligands from scratch for running in PMX. We obtained the SDF file for the ligand from the following reference: [[https://pubs.acs.org/doi/10.1021/ja512751q](https://pubs.acs.org/doi/10.1021/ja512751q)]

Our procedure was as follows:

1. Hydrogen atoms were added to the SDF file.

2. The file was converted to .mol2 format.

3. Acpype was used to generate the ligand input parameter files: ffMOL.itp, mol\_gmx.pdb, and MOL.itp. We used all available force fields within acpype: Amber, GAFF, and GAFF2.

4. We examined the generated .itp files and encountered the following issues:

We are using the same ligand as in the PMX tutorials, extracted from the reference article. Our question is: how can we generate .itp files with the same atom type representation and sigma/epsilon values as the PMX tutorials, using acpype or any other suitable tool?

For your review and guidance, we have pasted the ffMOL.itp file from the tutorial and the generated 18625-1- ffMOL.itp file (corresponding to the 18625-1 molecule) by us. We would greatly appreciate your assistance in determining the next steps.

Thank you for your time and help.

Thanks and regards

Jinuraj

ffMOL is shown below (From the pmx tutorial)  
[atomtypes]  
c 0.000000 0.000000 A 0.331521 0.413379  
ns 0.000000 0.000000 A 0.326995 0.491202  
cl 0.000000 0.000000 A 0.346595 1.103740  
ca 0.000000 0.000000 A 0.331521 0.413379  
h1 0.000000 0.000000 A 0.242200 0.087027  
cg 0.000000 0.000000 A 0.347896 0.667766  
o 0.000000 0.000000 A 0.304812 0.612119  
DU 0.000000 0.000000 A 0.000000 0.000000  
hn 0.000000 0.000000 A 0.110650 0.041840  
n1 0.000000 0.000000 A 0.327352 0.459403  
c3 0.000000 0.000000 A 0.339771 0.451035  
hc 0.000000 0.000000 A 0.260018 0.087027  
ha 0.000000 0.000000 A 0.262548 0.067362  
os 0.000000 0.000000 A 0.315610 0.303758  
nb 0.000000 0.000000 A 0.338417 0.393714  
nv 0.000000 0.000000 A 0.336813 0.468608

18625-1\_ffMOL is given below(Generated by acpype)  
[atomtypes]  
CT 0.000000 0.000000 A 0.339967 0.457730  
OS 0.000000 0.000000 A 0.300001 0.711280  
CA 0.000000 0.000000 A 0.339967 0.359824  
NC 0.000000 0.000000 A 0.325000 0.711280  
N2 0.000000 0.000000 A 0.325000 0.711280  
CM 0.000000 0.000000 A 0.339967 0.359824  
CZ 0.000000 0.000000 A 0.339967 0.359824  
N1 0.000000 0.000000 A 0.325000 0.711280  
C 0.000000 0.000000 A 0.339967 0.359824  
O 0.000000 0.000000 A 0.295992 0.878640  
Cl 0.000000 0.000000 A 0.347094 1.108760  
HC 0.000000 0.000000 A 0.264953 0.065689  
H1 0.000000 0.000000 A 0.247135 0.065689  
HA 0.000000 0.000000 A 0.259964 0.062760  
H 0.000000 0.000000 A 0.106908 0.065689

---

<div class="post-metadata">

**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [February 20, 2025, 12:30pm UTC](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429/2 "2025-02-20T12:30:07Z")

</div>

Ligand parameters in the tutorial were generated with acpype and gaff 2.1

The atom types that you pasted don’t seem to be from gaff, as they are in upper case. Could these be amber params?

Vytas

---

<div class="post-metadata">

**Author:** ![jinurajkr](https://avatars.discourse-cdn.com/v4/letter/j/d26b3c/32.png) [@jinurajkr](https://ask.bioexcel.eu/u/jinurajkr)\
**Post date:** [February 28, 2025, 11:49am UTC](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429/3 "2025-02-28T11:49:21Z")

</div>

Thanks you for your support . I could use gaff 2 force field to run it.  
Thanks and regards