Re: [gmx-users] genion doesn't recognize SOL in top file

2013-10-17 Thread Justin Lemkul 



On 10/17/13 1:01 PM, sunyeping wrote:

Dear Gromacs users,
I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro 
-p topol.top -pname NA -nname CL -np 8

but it returns a error message saying:

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file 
'topol.top'

I checked the topol.top file, but SOL is indeed under [ molecules ] section:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
DRG 1
SOL 86574

I know it problem has been disscussed here before, but I cann't fix it out with 
the avialable information. Could you help me with it?



You probably have a non-Unix newline character somewhere.  Run the .top file 
through dos2unix and try again.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] genion doesn't recognize SOL in top file

2013-10-17 Thread sunyeping 
Dear Gromacs users,
I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro 
-p topol.top -pname NA -nname CL -np 8

but it returns a error message saying:

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file 
'topol.top'

I checked the topol.top file, but SOL is indeed under [ molecules ] section:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
DRG 1
SOL 86574

I know it problem has been disscussed here before, but I cann't fix it out with 
the avialable information. Could you help me with it?

Thanks in advance.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

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