[gmx-users] MD in DMSO

MOLTENI at unisi.it MOLTENI at unisi.it
Wed Aug 28 14:07:21 CEST 2002

I am trying to run a MD simulation of a peptide in DMSO and I have some

If I run genbox with:
genbox -cp A2AXVI_1.gro -cs dmso -o A2AXVI_1_b4em.gro -p A2AXVI_1.top
("A2AXVI_1" is my molecule)

genbox seems to work, but the next step, grompp, gives an error like: 
"Fatal error: number of coordinates in coordinate file
(A2AXVI_1_b4em.gro, 3321) does not match topology (A2AXVI_1.top, 2534)"
and in fact I find that genbox had not added to the topology file a line
"SOL               N"

So my question is: how do I specify that the solvent I want to add is

Thanks in advance
Elena Molteni

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