==============Original message text=============== On Thu, 26 Jun 2008 2:50:36 pm CDT Sung Hyun Park wrote: >My guess would be that you chose the wrong options when you ran >pdb2gmx. If you were to choose the normal NH3+ and COO- options, you >will get the wrong charge. What you want is to choose the >Zwitterion-NH3+ and Zwitterion-COO- options with pdb2gmx. Those will >give the correct atom types and charges for a zwitterionic single amino >acid. > >-Justin You are perfectly correct! I chose the wrong options in pdb2gmx before. I just repeated pdb2gmx following your advice, and now the total charge for the protonated Lysine shows +1, the correct value. Thank you very much!! Now may I ask one more question? I was also doing the same simulation with a "neutral" Lysine, with the molecular formula (NH2)CH(COO-)(CH2)4NH3+, and was having a similar problem of non-integral total charge. Following the advice above, I repeated pdb2gmx for the neutral Lysine, this time by choosing NH2 for N-terminus and Zwitterion-COO- as C-terminus. Strangely it didn't solve the total charge problem this time, and the total charge is still non-integer at 0.13, instead of the correct value at zero.(shown below) What am I still doing wrong here? My command line and options chosen are as following (Lys.pdb is the input pdb file): ----------------------------------------------------------------------------------------- >pdb2gmx -f Lys.pdb -ter -n -p Select N-terminus type (start) 0: NH3+ 1: ZWITTERION_NH3+ 2: NH2 3: None >2 N-terminus: NH2 Select C-terminus type (end) 0: COO- 1: ZWITTERION_COO- 2: COOH 3: None >1 C-terminus: ZWITTERION_COO- ----------------------------------------------------------------------------------------- #include "ffoplsaa.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_900 1 LYSH N 1 -0.9 14.0067 ; qtot -0.9 2 opls_909 1 LYSH H1 1 0.36 1.008 ; qtot -0.54 3 opls_909 1 LYSH H2 1 0.36 1.008 ; qtot -0.18 4 opls_299 1 LYSH CA 1 0.15 12.011 ; qtot -0.03 5 opls_140 1 LYSH HA 1 0.06 1.008 ; qtot 0.03 6 opls_136 1 LYSH CB 2 -0.12 12.011 ; qtot -0.09 7 opls_140 1 LYSH HB1 2 0.06 1.008 ; qtot -0.03 8 opls_140 1 LYSH HB2 2 0.06 1.008 ; qtot 0.03 9 opls_136 1 LYSH CG 3 -0.12 12.011 ; qtot -0.09 10 opls_140 1 LYSH HG1 3 0.06 1.008 ; qtot -0.03 11 opls_140 1 LYSH HG2 3 0.06 1.008 ; qtot 0.03 12 opls_136 1 LYSH CD 4 -0.12 12.011 ; qtot -0.09 13 opls_140 1 LYSH HD1 4 0.06 1.008 ; qtot -0.03 14 opls_140 1 LYSH HD2 4 0.06 1.008 ; qtot 0.03 15 opls_292 1 LYSH CE 5 0.19 12.011 ; qtot 0.22 16 opls_140 1 LYSH HE1 5 0.06 1.008 ; qtot 0.28 17 opls_140 1 LYSH HE2 5 0.06 1.008 ; qtot 0.34 18 opls_287 1 LYSH NZ 6 -0.3 14.0067 ; qtot 0.04 19 opls_290 1 LYSH HZ1 6 0.33 1.008 ; qtot 0.37 20 opls_290 1 LYSH HZ2 6 0.33 1.008 ; qtot 0.7 21 opls_290 1 LYSH HZ3 6 0.33 1.008 ; qtot 1.03 22 opls_271 1 LYSH C 7 0.7 12.011 ; qtot 1.73 23 opls_272 1 LYSH O1 7 -0.8 15.9994 ; qtot 0.93 24 opls_272 1 LYSH O2 7 -0.8 15.9994 ; qtot 0.13 --------------------------------------------------------------------------------------------------- Sorry for many questions and many thanks in advance for your kind help! Regards, Sung Hyun ===========End of original message text=========== Oh, do I choose -NH2 for N-terminus and -COO- for C-terminus in case of a neutral Lysine? The total charge becomes 0.02 with such selections. If so, is the total charge 0.02 close enough to 0 (zero) to move on to the next step? Thanks and with regards, Sung Hyun