if gotras are same, the hindu marriage act and special marriage act has not prohibited the marriage. The prohibition of marriage is between the sapindas and between within the prohibited relationship. What is sapinda and what is within prohibited relationship is explained in the Act. if you will not come under this category, you can go for marriage. I reproduce it for ready reference.
(f) (i) "sapinda relationship" with reference to any
person extends as far as the third generation (inclusive) in
the line of ascent through the mother, and the fifth
(inclusive) in the line of ascent through the father, the
line being traced upwards in each case from the person
concerned, who is to be counted as the first generation;
(ii) two persons are said to be "sapindas" of each other if
one is a lineal ascendant of the other within the limits of
sapinda relationship, or if they have a common lineal
ascendant who is within the limits of sapinda relationship
with reference to each of them;
(g) "degrees of prohibited relationship"-two persons are
said to be within the "degrees of prohibited relationship"--
(i) if one is a lineal ascendant of the other; or
(ii) if one was the wife or husband of a lineal
ascendant or descendant of the other ; or
(iii) if one was the wife of the brother or of the
father's or mother's brother or of the grandfather's or
grandmother's brother of the other; or
(iv) if the two are brother and sister, uncle and
niece, aunt and nephew, or children of brother and
sister or of two brothers or of two sisters ;
Explanation.-For the purposes of clauses (f) and (g), relationship
includes-
(i) relationship by half or uterine blood as well as
by full blood;
(ii) illegitimate blood relationship as well as
legitimate;
(iii) relationship by adoption as well as by blood ; and
all terms of relationship in those clauses shall be
construed accordingly.