[gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp

Chris Neale chris.neale at utoronto.ca
Mon Mar 31 15:00:57 CEST 2008

There is no need to post twice, I saw your first post. Your level of questions indicates that you still do not understand the topology file format. It is essential that you understand exactly how it works and what is going on or else you are more likely to have errors in your simulation. I am happy to get you started, but when you encounter your next problem (probably regarding correct treatment of opls water oxygen?) you will be able to solve it yourself if you have taken the time to understand how this works.

1) Your [ atomtypes ] section should have:
    H        H     1    1.00800      0.400       A    0.00000e+00  0.00000e+00 ; opls_369

But then you can ignore H in other sections since the LJ is actually zero.


2) copy the entire pairs section and paste it under itself:

1 2
1 3

1 2
1 3
1 2
1 3



-- original message --

Hi all,
Two days back I posted this question, no one replied thats why I am posting
I wanted to use OPLS-AA/L force field for POPC and Protein
1.I calculated  the sigma and epsilon values as the way Mr.Justin mentioned
, the values I got are
 ;name   name   charge     mass   charge   ptype    sigma           epsilon
  LO      LO         1        15.9994   0.000      A    0.295999914
0.878694594 ;carbonyl O, OPLS
  LOM   LOM      1        15.9994   0.000      A     0.295999914
0.878694594 ;carboxyl O, OPLS
  LNL    LNL        1        14.0067   0.000     A     3.35300e-03
3.95100e-06 ;Nitrogen, OPLS

2. Then in first step of Chris procedure(web link quoted below), wrote that
add atom type H from opls_369 to match H expected by pope.itp
In archives H atom type adding problem posted for pope type of lipids
  opls_369   H    1   1.008  0.400     A     0.0000e+00   0.0000e+00 (for
 Im using POPC type of lipid
 I want to ask two things
1.  How can I  modify H atom type in popc.itp file
2. Mr. Chris mentioned that Parameters require a double pairs section,  how
can I mention?

Pls give me detail explanation, Eagerly  waiting for reply
all comments will be appreciated
Thanks in advance

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