[gmx-users] Cgenff generated force field problem

Justin Lemkul jalemkul at vt.edu
Sun Jun 16 01:39:39 CEST 2019

On 6/13/19 8:02 PM, Prabir Khatua wrote:
> Hi Gromacs Users,
> I am trying to do a protein-ligand simulation where the force field of the
> ligand has been generated by cgenff. I have manually edited the protein
> .top file, which has been generated  by pdb2gmx, by adding the lines
> #include .prm and #include .itp at appropriate positions. However, I am
> getting a list of warning while I am trying to prepare .tpr file like
> WARNING 10 [file lau.prm, line 43]:
>    Overriding Proper Dih. parameters.
>    Use dihedraltype 9 to allow several multiplicity terms. Only consecutive
>    lines are combined. Non-consective lines overwrite each other.
>    old:                                          0 0.452709 4 0 0.452709 4
>    new: CG321    CG321    CG321    CG331     9     0.000000     0.853118
> 5
> After careful examination, I have come to know that this is happening due
> to the fact that these are already there in the parent force field file.
> However, I have some dihedral angle force field parameters for the ligand
> with same atom type, multiplicty as that of the protein but a slight
> variation in the value of kphi. Therefore, I think I probably have to
> delete the lines that are exactly matching with that of parent protein
> force field from the ligand prm file and to keep the lines those are not
> matching. I am wondering whether doing this will solve my problem and will
> not have any impact on the results. Please suggest me whether I am going to
> do the right thing or I should do something else. Any help would be
> appreciated.

The parameter from the parent force field should be used, but be careful 
because apparently your topology does not make use of the same CGenFF 
version as the C36 port. The online server tends to be somewhat outdated 
relative to what we can provide via our force field port. Thus, some 
parameters may have changed between versions.


> Thanks in advance,
> Prabir


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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