ligparfen failed about ligpargen

[leelasd]

@zhouyu8791 Please elaborate more. What net charge did you use? It works fine for me with charge of -1 but fails with -2 charge. So please check your structures and make sure you are using the right charges (you can use chimera to see what is the net charge on the molecule).

Hope this helps.

[zhouyu8791]

for MDA and MDC, net charge is -1, and for MAB, net charge is -2. However, three were failed for me ...

[leelasd]

@zhouyu8791 Can I close this issue ?

[Muneeb-Aliyarhussain]

Doc2.docx
I am trying to get topology files of GROMACS (.itp and .top) for my compound using the LigParnGen web server. I have tried everything but was not able to do so. therefore kind help me in this respect.
Find the attachment, please.
thanks.

[leelasd]

@Muneeb-Aliyarhussain You have not added the hydrogens to molecule. Please read the paper to know how LigParGen works. Only requirement to make it work is to have an accurate molecule input file, whether its MOL/PDB (hydrogens should be added) or Smiles code.
Your input seems to have met none of the requirements. So please fix it and upload your input.

[Muneeb-Aliyarhussain]

Dear Sir, I have tried SMILES .mol and .pdb along with all hydrogens but I am not getting any result. I will be greatly thankful for this act of kindness. thanks. SMILES. O(CCCCCCCCCCCCCCCC)c1ccc(C2c3c(O)cc(O)c(C(c4ccc(OCCCCCCCCCCCCCCCC)cc4)c4c(O)cc(O)c(C(c5ccc(OCCCCCCCCCCCCCCCC)cc5)c5c(O)cc(O)c(C(c6ccc(OCCCCCCCCCCCCCCCC)cc6)c6c(O)cc(O)c2c6)c5)c4)c3)cc1 With Best Regards, *Muneeb Ali,* *Jr. Research Fellow,* *Lab No. P-133, Computational Chemistry Unit,* *Dr. Panjwani Center for Molecular Medicine and Drug Research,* *International Center for Chemical and Biological Science,* *The University of Karachi-75270,* *Karachi-Pakistan* http://sites.google.com/site/zaheerqasmi/groupmember

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