# Different masses of dummy atoms in webserver pmx and standalone pmx **URL:** \ **Category:** pmx\ **Created:** [October 18, 2023, 2:06pm UTC](https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612 "2023-10-18T14:06:56Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Mary](https://avatars.discourse-cdn.com/v4/letter/m/e99b99/32.png) [@Mary](https://ask.bioexcel.eu/u/Mary)\ **Post date:** [October 18, 2023, 2:06pm UTC](https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612/1 "2023-10-18T14:06:57Z")
Dear Gromacs users, I am trying to calculate ddG of folding of barnase mutant H18D (barnase ID: 1BNI) using FEP with double system/single box protocol. While generating hybrid structures for barnase and tripeptide I noticed that there is the difference of mass values for dummy atoms in itp files generated in pmx webserver and latest pmx version from GitHub ([GitHub - deGrootLab/pmx: Toolkit for free-energy calculation setup/analysis and biomolecular structure handling](https://github.com/deGrootLab/pmx)). Here are mass values of dummy atoms for 18H2D residue itp generated in pmx webserver: 235 N 18 H2D N 235 -0.415700 14.0100 N -0.516300 14.0100 236 H 18 H2D H 236 0.271900 1.0080 H 0.293600 1.0080 237 CT 18 H2D CA 237 0.018800 12.0100 CT 0.038100 12.0100 238 H1 18 H2D HA 238 0.088100 1.0080 H1 0.088000 1.0080 239 CT 18 H2D CB 239 -0.046200 12.0100 CT -0.030300 12.0100 240 HC 18 H2D HB1 240 0.040200 1.0080 HC -0.012200 1.0080 241 HC 18 H2D HB2 241 0.040200 1.0080 HC -0.012200 1.0080 242 **CC 18 H2D CG 242 -0.026600 12.0100 DUM\_CC 0.000000 1.0000** \*\* 243 NA 18 H2D ND1 243 -0.381100 14.0100 DUM\_NA 0.000000 1.0000\*\* \*\* 244 H 18 H2D HD1 244 0.364900 1.0080 DUM\_H 0.000000 1.0000\*\* \*\* 245 CV 18 H2D CD2 245 0.129200 12.0100 DUM\_CV 0.000000 1.0000\*\* \*\* 246 H4 18 H2D HD2 246 0.114700 1.0080 DUM\_H4 0.000000 1.0000\*\* \*\* 247 CR 18 H2D CE1 247 0.205700 12.0100 DUM\_CR 0.000000 1.0000\*\* \*\* 248 H5 18 H2D HE1 248 0.139200 1.0080 DUM\_H5 0.000000 1.0000\*\* \*\* 249 NB 18 H2D NE2 249 -0.572700 14.0100 DUM\_NB 0.000000 1.0000\*\* 250 C 18 H2D C 250 0.597300 12.0100 C 0.536600 12.0100 251 O 18 H2D O 251 -0.567900 16.0000 O -0.581900 16.0000 252 **DUM\_C 18 H2D DCG 252 0.000000 1.0000 C 0.799400 12.0100** \*\* 253DUM\_O2 18 H2D DOD1 253 0.000000 1.0000 O2 -0.801400 16.0000\*\* \*\* 254DUM\_O2 18 H2D DOD2 254 0.000000 1.0000 O2 -0.801400 16.0000\*\* For all dummy atoms mass values are equal to 1 Here are mass values of dummy atoms for 18H2D residue itp generated with generate\_hybrid\_topology.py script from standalone pmx from GitHub: 235 N 18 H2D N 235 -0.415700 14.0100 N -0.516300 14.0100 236 H 18 H2D H 236 0.271900 1.0080 H 0.293600 1.0080 237 CT 18 H2D CA 237 0.018800 12.0100 CT 0.038100 12.0100 238 H1 18 H2D HA 238 0.088100 1.0080 H1 0.088000 1.0080 239 CT 18 H2D CB 239 -0.046200 12.0100 CT -0.030300 12.0100 240 HC 18 H2D HB1 240 0.040200 1.0080 HC -0.012200 1.0080 241 HC 18 H2D HB2 241 0.040200 1.0080 HC -0.012200 1.0080 **242 CC 18 H2D CG 242 -0.026600 12.0100 DUM\_CC 0.000000 3.9633** \*\* 243 NA 18 H2D ND1 243 -0.381100 14.0100 DUM\_NA 0.000000 4.6233\*\* \*\* 244 H 18 H2D HD1 244 0.364900 1.0080 DUM\_H 0.000000 1.0000\*\* \*\* 245 CV 18 H2D CD2 245 0.129200 12.0100 DUM\_CV 0.000000 3.9633\*\* \*\* 246 H4 18 H2D HD2 246 0.114700 1.0080 DUM\_H4 0.000000 1.0000\*\* \*\* 247 CR 18 H2D CE1 247 0.205700 12.0100 DUM\_CR 0.000000 3.9633\*\* \*\* 248 H5 18 H2D HE1 248 0.139200 1.0080 DUM\_H5 0.000000 1.0000\*\* \*\* 249 NB 18 H2D NE2 249 -0.572700 14.0100 DUM\_NB 0.000000 4.6233\*\* 250 C 18 H2D C 250 0.597300 12.0100 C 0.536600 12.0100 251 O 18 H2D O 251 -0.567900 16.0000 O -0.581900 16.0000 **252 DUM\_C 18 H2D DCG 252 0.000000 3.9633 C 0.799400 12.0100** \*\* 253 DUM\_O2 18 H2D DOD1 253 0.000000 5.2800 O2 -0.801400 16.0000\*\* \*\* 254 DUM\_O2 18 H2D DOD2 254 0.000000 5.2800 O2 -0.801400 16.0000\*\* Here mass values are different from 1 for non-hydrogen atoms. Did you implement some scaling factor for masses for a standalone version of pmx? How to define this scaling factor and which itp should I use? I assume this detail may drastically affect the ddG prediction results. I am a new user so I cannot upload full itp files in any way, but hopefully I will be able to do that in a discussion. Thank you all in advance! ---
**Author:** ![Sudchem](https://avatars.discourse-cdn.com/v4/letter/s/ecccb3/32.png) [@Sudchem](https://ask.bioexcel.eu/u/Sudchem)\ **Post date:** [October 31, 2023, 9:08am UTC](https://ask.bioexcel.eu/t/different-masses-of-dummy-atoms-in-webserver-pmx-and-standalone-pmx/4612/2 "2023-10-31T09:08:27Z")
Hi Mary, The recent version of pmx (develop branch) applies a scaling factor of 0.33 by default. Hence, the DUM\_C has a mass of 12.01\*0.33=3.9633. The web server uses an old version of pmx, in which the mass of a dummy is 1.0 by default. The scaling factor is used to maintain the stability of a simulated system. You can read this thread for more on the discussion: [Oscillational period warning during tripeptide A2I forward simulation](https://ask.bioexcel.eu/t/oscillational-period-warning-during-tripeptide-a2i-forward-simulation/4034) Using either of the itp files should be fine provided that your simulation is stable (no oscillation-period-warning). The mass of the dummy particle will not have much effect on the ddG prediction. Best, Sudarshan